{"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    469      0 --:--:-- --:--:-- --:--:--   469\n\r100  294k  100  294k    0     0   707k      0 --:--:-- --:--:-- --:--:--  707k\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 (22.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (62.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000411_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000411_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 236.4 KiB/236.4 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/outputs/reports.h5\nCompleted 219.8 KiB/242.0 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/output.zip\nCompleted 219.8 KiB/242.0 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 231.1 KiB/242.0 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000411_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/outputs/BIOMD0000000411_url.sedml/autogen_plot_for_task1.pdf\nCompleted 231.1 KiB/242.0 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 233.7 KiB/242.0 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/rawLog.txt\nCompleted 233.7 KiB/242.0 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 242.0 KiB/242.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000411-biopax2.owl  \n  inflating: contents/BIOMD0000000411-biopax3.owl  \n  inflating: contents/BIOMD0000000411-matlab.m  \n  inflating: contents/BIOMD0000000411-octave.m  \n  inflating: contents/BIOMD0000000411.m  \n  inflating: contents/BIOMD0000000411.ode  \n  inflating: contents/BIOMD0000000411.pdf  \n  inflating: contents/BIOMD0000000411.png  \n  inflating: contents/BIOMD0000000411.svg  \n  inflating: contents/BIOMD0000000411.vcml  \n  inflating: contents/BIOMD0000000411_url.sedml  \n  inflating: contents/BIOMD0000000411_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 32.5 KiB/617.5 KiB (430.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000411-biopax3.owl to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411-biopax3.owl\nCompleted 32.5 KiB/617.5 KiB (430.9 KiB/s) with 15 file(s) remaining\rCompleted 42.0 KiB/617.5 KiB (403.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000411-matlab.m to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411-matlab.m\nCompleted 42.0 KiB/617.5 KiB (403.6 KiB/s) with 14 file(s) remaining\rCompleted 51.4 KiB/617.5 KiB (409.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000411-octave.m to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411-octave.m\nCompleted 51.4 KiB/617.5 KiB (409.6 KiB/s) with 13 file(s) remaining\rCompleted 72.2 KiB/617.5 KiB (559.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000411-biopax2.owl to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411-biopax2.owl\nCompleted 72.2 KiB/617.5 KiB (559.7 KiB/s) with 12 file(s) remaining\rCompleted 98.6 KiB/617.5 KiB (713.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000411.svg to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.svg\nCompleted 98.6 KiB/617.5 KiB (713.9 KiB/s) with 11 file(s) remaining\rCompleted 172.2 KiB/617.5 KiB (1.1 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000411.vcml to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.vcml\nCompleted 172.2 KiB/617.5 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 193.5 KiB/617.5 KiB (1.2 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000411_url.sedml to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411_url.sedml\nCompleted 193.5 KiB/617.5 KiB (1.2 MiB/s) with 9 file(s) remaining\rCompleted 261.9 KiB/617.5 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000411_url.xml to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411_url.xml\nCompleted 261.9 KiB/617.5 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 266.1 KiB/617.5 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/metadata.rdf\nCompleted 266.1 KiB/617.5 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 275.6 KiB/617.5 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000411.m to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.m\nCompleted 275.6 KiB/617.5 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 275.9 KiB/617.5 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/curation_notes.txt\nCompleted 275.9 KiB/617.5 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 501.1 KiB/617.5 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000411.pdf to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.pdf\nCompleted 501.1 KiB/617.5 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 557.5 KiB/617.5 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000411.png to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.png\nCompleted 557.5 KiB/617.5 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 609.0 KiB/617.5 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/curation_image.png\nCompleted 609.0 KiB/617.5 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 610.8 KiB/617.5 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/manifest.xml\nCompleted 610.8 KiB/617.5 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 617.5 KiB/617.5 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000411.ode to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/contents/BIOMD0000000411.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (139.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5149c0d898ffde307b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000411_url.sedml\ncreating dataset /BIOMD0000000411_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-164f2651-b11fe622-9db2-7c3beb-f340ae, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000411_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\ndataset created, uuid: d-164f2651-b11fe622-6a43-bca182-9b88b8, chunk_size: (37, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000411_url.sedml\ncreating attribute uri in /BIOMD0000000411_url.sedml\ncreating attribute _type in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000411_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000411_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000411_url.sedml\ncreate_links: /BIOMD0000000411_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000411_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000411_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000411_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000411_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000411_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000411_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\niterating over chunks for /BIOMD0000000411_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 37, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000411_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c5149c0d898ffde307b\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 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.\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":22.339581,"sedDocuments":[{"location":"BIOMD0000000411_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  BIOMD0000000411_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000411_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":21.998269,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.244431,"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":0.273394,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_s2","status":"SUCCEEDED"},{"id":"autogen_task1_s9","status":"SUCCEEDED"},{"id":"autogen_task1_s10","status":"SUCCEEDED"},{"id":"autogen_task1_s11","status":"SUCCEEDED"},{"id":"autogen_task1_s13","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_task1_species_12","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_T2","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_1","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_2","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_3","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_4","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_5","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_6","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_7","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_8","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_9","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_10","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_re12","status":"SUCCEEDED"},{"id":"autogen_task1_re13","status":"SUCCEEDED"},{"id":"autogen_task1_re14","status":"SUCCEEDED"},{"id":"autogen_task1_re15","status":"SUCCEEDED"},{"id":"autogen_task1_re16","status":"SUCCEEDED"},{"id":"autogen_task1_re18","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_task1_reaction_7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.321533,"curves":[{"id":"autogen_curve_task1_s2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_s9","status":"SUCCEEDED"},{"id":"autogen_curve_task1_s10","status":"SUCCEEDED"},{"id":"autogen_curve_task1_s11","status":"SUCCEEDED"},{"id":"autogen_curve_task1_s13","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_12","status":"SUCCEEDED"}]}]}]}