{"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    462      0 --:--:-- --:--:-- --:--:--   461\n\r100  260k  100  260k    0     0   592k      0 --:--:-- --:--:-- --:--:--  592k\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 (28.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (56.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000035_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000035_url.sedml/autogen_plot_for_task1.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/270.8 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 270.8 KiB/270.8 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/outputs/reports.h5\nCompleted 256.0 KiB/284.9 KiB (6.4 MiB/s) with 4 file(s) remaining\rCompleted 259.6 KiB/284.9 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/output.zip\nCompleted 259.6 KiB/284.9 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 262.4 KiB/284.9 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/rawLog.txt\nCompleted 262.4 KiB/284.9 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 271.9 KiB/284.9 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/outputs/plots.zip\nCompleted 271.9 KiB/284.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 284.9 KiB/284.9 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000035_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/outputs/BIOMD0000000035_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/BIOMD0000000035-biopax2.owl  \n  inflating: contents/BIOMD0000000035-biopax3.owl  \n  inflating: contents/BIOMD0000000035-matlab.m  \n  inflating: contents/BIOMD0000000035-octave.m  \n  inflating: contents/BIOMD0000000035.m  \n  inflating: contents/BIOMD0000000035.ode  \n  inflating: contents/BIOMD0000000035.pdf  \n  inflating: contents/BIOMD0000000035.png  \n  inflating: contents/BIOMD0000000035.sci  \n  inflating: contents/BIOMD0000000035.svg  \n  inflating: contents/BIOMD0000000035.vcml  \n  inflating: contents/BIOMD0000000035_url.sedml  \n  inflating: contents/BIOMD0000000035_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 27.0 KiB/558.3 KiB (353.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000035-biopax2.owl to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035-biopax2.owl\nCompleted 27.0 KiB/558.3 KiB (353.3 KiB/s) with 16 file(s) remaining\rCompleted 33.8 KiB/558.3 KiB (307.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000035-octave.m to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035-octave.m\nCompleted 33.8 KiB/558.3 KiB (307.1 KiB/s) with 15 file(s) remaining\rCompleted 40.6 KiB/558.3 KiB (365.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000035-matlab.m to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035-matlab.m\nCompleted 40.6 KiB/558.3 KiB (365.1 KiB/s) with 14 file(s) remaining\rCompleted 45.1 KiB/558.3 KiB (332.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000035.sci to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.sci\nCompleted 45.1 KiB/558.3 KiB (332.4 KiB/s) with 13 file(s) remaining\rCompleted 45.1 KiB/558.3 KiB (322.6 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/curation_notes.txt\nCompleted 45.1 KiB/558.3 KiB (322.6 KiB/s) with 12 file(s) remaining\rCompleted 133.5 KiB/558.3 KiB (941.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000035.png to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.png\nCompleted 133.5 KiB/558.3 KiB (941.4 KiB/s) with 11 file(s) remaining\rCompleted 166.3 KiB/558.3 KiB (1.1 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000035.svg to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.svg\nCompleted 166.3 KiB/558.3 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 174.8 KiB/558.3 KiB (1.0 MiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/metadata.rdf\nCompleted 174.8 KiB/558.3 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 191.5 KiB/558.3 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000035_url.sedml to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035_url.sedml\nCompleted 191.5 KiB/558.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 193.5 KiB/558.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/manifest.xml\nCompleted 193.5 KiB/558.3 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 249.1 KiB/558.3 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000035.vcml to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.vcml\nCompleted 249.1 KiB/558.3 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 268.0 KiB/558.3 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/curation_image.png\nCompleted 268.0 KiB/558.3 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 303.0 KiB/558.3 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000035_url.xml to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035_url.xml\nCompleted 303.0 KiB/558.3 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 309.8 KiB/558.3 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000035.m to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.m\nCompleted 309.8 KiB/558.3 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 353.5 KiB/558.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000035-biopax3.owl to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035-biopax3.owl\nCompleted 353.5 KiB/558.3 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 554.2 KiB/558.3 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000035.pdf to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.pdf\nCompleted 554.2 KiB/558.3 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 558.3 KiB/558.3 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000035.ode to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/contents/BIOMD0000000035.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (147.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107650dcacb55678b3f67/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000035_url.sedml\ncreating dataset /BIOMD0000000035_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-758c9bbd-3e791019-c555-65c557-d68f29, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000035_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-758c9bbd-3e791019-9a11-82e9cd-7d0db8, chunk_size: (28, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000035_url.sedml\ncreating attribute uri in /BIOMD0000000035_url.sedml\ncreating attribute _type in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000035_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000035_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000035_url.sedml\ncreate_links: /BIOMD0000000035_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000035_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000035_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000035_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000035_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000035_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000035_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000035_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000035_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107650dcacb55678b3f67\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.\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":16.686904,"sedDocuments":[{"location":"BIOMD0000000035_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  BIOMD0000000035_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000035_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":16.398907,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":15.553776,"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":0.240672,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_DA","status":"SUCCEEDED"},{"id":"autogen_task1_DAp","status":"SUCCEEDED"},{"id":"autogen_task1_DR","status":"SUCCEEDED"},{"id":"autogen_task1_DRp","status":"SUCCEEDED"},{"id":"autogen_task1_MA","status":"SUCCEEDED"},{"id":"autogen_task1_MR","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_deterministicOscillator","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_Reaction13","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction14","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction15","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction16","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.483665,"curves":[{"id":"autogen_curve_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DAp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DRp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"}]}]}]}