{"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    441      0 --:--:-- --:--:-- --:--:--   441\n\r100  364k  100  364k    0     0   831k      0 --:--:-- --:--:-- --:--:--  831k\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 (24.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/rawLog.txt\nCompleted 5.2 KiB/5.2 KiB (49.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: outputs/BIOMD0000000022_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000022_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/414.4 KiB (4.7 MiB/s) with 1 file(s) remaining\rCompleted 414.4 KiB/414.4 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/outputs/reports.h5\nCompleted 256.0 KiB/429.5 KiB (5.8 MiB/s) with 4 file(s) remaining\rCompleted 399.1 KiB/429.5 KiB (3.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/output.zip\nCompleted 399.1 KiB/429.5 KiB (3.9 MiB/s) with 3 file(s) remaining\rCompleted 410.9 KiB/429.5 KiB (3.9 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/outputs/plots.zip\nCompleted 410.9 KiB/429.5 KiB (3.9 MiB/s) with 2 file(s) remaining\rCompleted 413.6 KiB/429.5 KiB (3.4 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/rawLog.txt\nCompleted 413.6 KiB/429.5 KiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 429.5 KiB/429.5 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000022_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/outputs/BIOMD0000000022_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000022-biopax2.owl  \n  inflating: contents/BIOMD0000000022-biopax3.owl  \n  inflating: contents/BIOMD0000000022-matlab.m  \n  inflating: contents/BIOMD0000000022-octave.m  \n  inflating: contents/BIOMD0000000022.m  \n  inflating: contents/BIOMD0000000022.ode  \n  inflating: contents/BIOMD0000000022.pdf  \n  inflating: contents/BIOMD0000000022.png  \n  inflating: contents/BIOMD0000000022.sci  \n  inflating: contents/BIOMD0000000022.svg  \n  inflating: contents/BIOMD0000000022_url.sedml  \n  inflating: contents/BIOMD0000000022_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 71.6 KiB/799.7 KiB (963.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000022-biopax3.owl to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022-biopax3.owl\nCompleted 71.6 KiB/799.7 KiB (963.8 KiB/s) with 15 file(s) remaining\rCompleted 87.1 KiB/799.7 KiB (773.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000022-matlab.m to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022-matlab.m\nCompleted 87.1 KiB/799.7 KiB (773.3 KiB/s) with 14 file(s) remaining\rCompleted 87.1 KiB/799.7 KiB (645.2 KiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/curation_notes.txt\nCompleted 87.1 KiB/799.7 KiB (645.2 KiB/s) with 13 file(s) remaining\rCompleted 131.0 KiB/799.7 KiB (902.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000022-biopax2.owl to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022-biopax2.owl\nCompleted 131.0 KiB/799.7 KiB (902.5 KiB/s) with 12 file(s) remaining\rCompleted 146.5 KiB/799.7 KiB (963.3 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000022-octave.m to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022-octave.m\nCompleted 146.5 KiB/799.7 KiB (963.3 KiB/s) with 11 file(s) remaining\rCompleted 157.3 KiB/799.7 KiB (997.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000022.sci to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.sci\nCompleted 157.3 KiB/799.7 KiB (997.2 KiB/s) with 10 file(s) remaining\rCompleted 185.6 KiB/799.7 KiB (1.1 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000022_url.sedml to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022_url.sedml\nCompleted 185.6 KiB/799.7 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 441.6 KiB/799.7 KiB (2.6 MiB/s) with 9 file(s) remaining\rCompleted 514.4 KiB/799.7 KiB (2.9 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000022.svg to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.svg\nCompleted 514.4 KiB/799.7 KiB (2.9 MiB/s) with 8 file(s) remaining\rCompleted 517.8 KiB/799.7 KiB (2.8 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/metadata.rdf\nCompleted 517.8 KiB/799.7 KiB (2.8 MiB/s) with 7 file(s) remaining\rCompleted 582.3 KiB/799.7 KiB (3.0 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000022_url.xml to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022_url.xml\nCompleted 582.3 KiB/799.7 KiB (3.0 MiB/s) with 6 file(s) remaining\rCompleted 584.1 KiB/799.7 KiB (2.9 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/manifest.xml\nCompleted 584.1 KiB/799.7 KiB (2.9 MiB/s) with 5 file(s) remaining\rCompleted 603.6 KiB/799.7 KiB (2.9 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/curation_image.png\nCompleted 603.6 KiB/799.7 KiB (2.9 MiB/s) with 4 file(s) remaining\rCompleted 619.1 KiB/799.7 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000022.m to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.m\nCompleted 619.1 KiB/799.7 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 628.8 KiB/799.7 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000022.ode to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.ode\nCompleted 628.8 KiB/799.7 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 645.6 KiB/799.7 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000022.pdf to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.pdf\nCompleted 645.6 KiB/799.7 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 799.7 KiB/799.7 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000022.png to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/contents/BIOMD0000000022.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (99.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073d0dcacb55678b3b12/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000022_url.sedml\ncreating dataset /BIOMD0000000022_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-12dbf7ac-6cf0e4a5-def8-8e2b70-14c552, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000022_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\ndataset created, uuid: d-12dbf7ac-6cf0e4a5-84e7-a54db5-f82ab9, chunk_size: (49, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000022_url.sedml\ncreating attribute uri in /BIOMD0000000022_url.sedml\ncreating attribute _type in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000022_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000022_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000022_url.sedml\ncreate_links: /BIOMD0000000022_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000022_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000022_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000022_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000022_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000022_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000022_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\niterating over chunks for /BIOMD0000000022_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 49, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000022_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471073d0dcacb55678b3b12\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 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 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.\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":24.511187,"sedDocuments":[{"location":"BIOMD0000000022_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  BIOMD0000000022_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 49 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000022_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":24.130901,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":23.109916,"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":0.408631,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_CCc","status":"SUCCEEDED"},{"id":"autogen_task1_CCn","status":"SUCCEEDED"},{"id":"autogen_task1_Clkc","status":"SUCCEEDED"},{"id":"autogen_task1_Clkm","status":"SUCCEEDED"},{"id":"autogen_task1_Perc","status":"SUCCEEDED"},{"id":"autogen_task1_Perm","status":"SUCCEEDED"},{"id":"autogen_task1_PTc","status":"SUCCEEDED"},{"id":"autogen_task1_PTn","status":"SUCCEEDED"},{"id":"autogen_task1_Timc","status":"SUCCEEDED"},{"id":"autogen_task1_Timm","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000012","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000013","status":"SUCCEEDED"},{"id":"autogen_task1_Drosophilia","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000003","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000002","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_task1_Reaction8","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction9","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction10","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction11","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction12","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction16","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction18","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction19","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction20","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction21","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction23","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction24","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction25","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction26","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction27","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction28","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction29","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction30","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction31","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction32","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction33","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction34","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction35","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction36","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction37","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.447133,"curves":[{"id":"autogen_curve_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CCc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CCn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Clkc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Clkm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Perc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Perm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PTc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PTn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Timc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Timm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000012","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000013","status":"SUCCEEDED"}]}]}]}