{"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    436      0 --:--:-- --:--:-- --:--:--   435\n\r100  209k  100  209k    0     0   450k      0 --:--:-- --:--:-- --:--:--  450k\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 (15.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/rawLog.txt\nCompleted 2.7 KiB/2.7 KiB (30.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: outputs/BIOMD0000000003_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000003_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 132.2 KiB/132.2 KiB (802.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/outputs/reports.h5\nCompleted 118.6 KiB/135.5 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/output.zip\nCompleted 118.6 KiB/135.5 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 127.2 KiB/135.5 KiB (905.3 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000003_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/outputs/BIOMD0000000003_url.sedml/autogen_plot_for_task1.pdf\nCompleted 127.2 KiB/135.5 KiB (905.3 KiB/s) with 2 file(s) remaining\rCompleted 129.9 KiB/135.5 KiB (829.2 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/rawLog.txt\nCompleted 129.9 KiB/135.5 KiB (829.2 KiB/s) with 1 file(s) remaining\rCompleted 135.5 KiB/135.5 KiB (818.7 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000003-biopax2.owl  \n  inflating: contents/BIOMD0000000003-biopax3.owl  \n  inflating: contents/BIOMD0000000003-matlab.m  \n  inflating: contents/BIOMD0000000003-octave.m  \n  inflating: contents/BIOMD0000000003.m  \n  inflating: contents/BIOMD0000000003.pdf  \n  inflating: contents/BIOMD0000000003.png  \n  inflating: contents/BIOMD0000000003.sci  \n  inflating: contents/BIOMD0000000003.svg  \n  inflating: contents/BIOMD0000000003.vcml  \n  inflating: contents/BIOMD0000000003_manual.png  \n  inflating: contents/BIOMD0000000003_manual.svg  \n  inflating: contents/BIOMD0000000003_url.sedml  \n  inflating: contents/BIOMD0000000003_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 12.6 KiB/~356.8 KiB (187.6 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000003-biopax2.owl to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003-biopax2.owl\nCompleted 12.6 KiB/~356.8 KiB (187.6 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 17.3 KiB/377.8 KiB (142.1 KiB/s) with 17 file(s) remaining                   \rupload: contents/BIOMD0000000003-matlab.m to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003-matlab.m\nCompleted 17.3 KiB/377.8 KiB (142.1 KiB/s) with 16 file(s) remaining\rCompleted 33.3 KiB/377.8 KiB (265.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000003-biopax3.owl to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003-biopax3.owl\nCompleted 33.3 KiB/377.8 KiB (265.9 KiB/s) with 15 file(s) remaining\rCompleted 53.7 KiB/377.8 KiB (365.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000003.svg to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.svg\nCompleted 53.7 KiB/377.8 KiB (365.3 KiB/s) with 14 file(s) remaining\rCompleted 58.5 KiB/377.8 KiB (374.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000003-octave.m to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003-octave.m\nCompleted 58.5 KiB/377.8 KiB (374.2 KiB/s) with 13 file(s) remaining\rCompleted 79.8 KiB/377.8 KiB (489.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000003_url.xml to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003_url.xml\nCompleted 79.8 KiB/377.8 KiB (489.6 KiB/s) with 12 file(s) remaining\rCompleted 106.9 KiB/377.8 KiB (646.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000003.vcml to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.vcml\nCompleted 106.9 KiB/377.8 KiB (646.8 KiB/s) with 11 file(s) remaining\rCompleted 131.2 KiB/377.8 KiB (770.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000003_manual.png to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003_manual.png\nCompleted 131.2 KiB/377.8 KiB (770.9 KiB/s) with 10 file(s) remaining\rCompleted 151.6 KiB/377.8 KiB (871.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000003_manual.svg to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003_manual.svg\nCompleted 151.6 KiB/377.8 KiB (871.1 KiB/s) with 9 file(s) remaining\rCompleted 153.7 KiB/377.8 KiB (821.7 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/manifest.xml\nCompleted 153.7 KiB/377.8 KiB (821.7 KiB/s) with 8 file(s) remaining\rCompleted 153.8 KiB/377.8 KiB (818.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/curation_notes.txt\nCompleted 153.8 KiB/377.8 KiB (818.1 KiB/s) with 7 file(s) remaining\rCompleted 163.7 KiB/377.8 KiB (792.5 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000003_url.sedml to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003_url.sedml\nCompleted 163.7 KiB/377.8 KiB (792.5 KiB/s) with 6 file(s) remaining\rCompleted 168.7 KiB/377.8 KiB (761.1 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/metadata.rdf\nCompleted 168.7 KiB/377.8 KiB (761.1 KiB/s) with 5 file(s) remaining\rCompleted 173.5 KiB/377.8 KiB (777.1 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000003.m to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.m\nCompleted 173.5 KiB/377.8 KiB (777.1 KiB/s) with 4 file(s) remaining\rCompleted 187.3 KiB/377.8 KiB (833.4 KiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/curation_image.png\nCompleted 187.3 KiB/377.8 KiB (833.4 KiB/s) with 3 file(s) remaining\rCompleted 211.6 KiB/377.8 KiB (899.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000003.png to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.png\nCompleted 211.6 KiB/377.8 KiB (899.1 KiB/s) with 2 file(s) remaining\rCompleted 213.9 KiB/377.8 KiB (902.2 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000003.sci to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.sci\nCompleted 213.9 KiB/377.8 KiB (902.2 KiB/s) with 1 file(s) remaining\rCompleted 377.8 KiB/377.8 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000003.pdf to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/contents/BIOMD0000000003.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.6 KiB/9.6 KiB (90.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f749c0d898ffdd8d68/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000003_url.sedml\ncreating dataset /BIOMD0000000003_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-ae0297aa-3b180e5b-0193-6155b0-f52a9e, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000003_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-ae0297aa-3b180e5b-df6f-9eaed4-141fd8, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000003_url.sedml\ncreating attribute uri in /BIOMD0000000003_url.sedml\ncreating attribute _type in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000003_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000003_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000003_url.sedml\ncreate_links: /BIOMD0000000003_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000003_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000003_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000003_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000003_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000003_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000003_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000003_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000003_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647106f749c0d898ffdd8d68\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.041765,"sedDocuments":[{"location":"BIOMD0000000003_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  BIOMD0000000003_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000003_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":19.744973,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.171746,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.180548,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_V3","status":"SUCCEEDED"},{"id":"autogen_task1_VM1","status":"SUCCEEDED"},{"id":"autogen_task1_VM3","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.264187,"curves":[{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"}]}]}]}