{"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    448      0 --:--:-- --:--:-- --:--:--   449\n\r100  471k  100  471k    0     0  1040k      0 --:--:-- --:--:-- --:--:-- 1040k\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 (23.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (54.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/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/reports.h5 (deflated 11%)\n  adding: outputs/BIOMD0000000440_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000440_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 213.1 KiB/213.1 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/outputs/reports.h5\nCompleted 7.0 KiB/219.1 KiB (68.6 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/outputs/plots.zip\nCompleted 7.0 KiB/219.1 KiB (68.6 KiB/s) with 3 file(s) remaining\rCompleted 206.2 KiB/219.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/output.zip\nCompleted 206.2 KiB/219.1 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 216.4 KiB/219.1 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000440_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/outputs/BIOMD0000000440_url.sedml/autogen_plot_for_task1.pdf\nCompleted 216.4 KiB/219.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 219.1 KiB/219.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000440-biopax2.owl  \n  inflating: contents/BIOMD0000000440-biopax3.owl  \n  inflating: contents/BIOMD0000000440-matlab.m  \n  inflating: contents/BIOMD0000000440.m  \n  inflating: contents/BIOMD0000000440.ode  \n  inflating: contents/BIOMD0000000440.pdf  \n  inflating: contents/BIOMD0000000440.png  \n  inflating: contents/BIOMD0000000440.svg  \n  inflating: contents/BIOMD0000000440.vcml  \n  inflating: contents/BIOMD0000000440_url.sedml  \n  inflating: contents/BIOMD0000000440_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 31.9 KiB/805.0 KiB (420.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000440-biopax3.owl to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440-biopax3.owl\nCompleted 31.9 KiB/805.0 KiB (420.7 KiB/s) with 14 file(s) remaining\rCompleted 41.2 KiB/805.0 KiB (374.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000440-matlab.m to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440-matlab.m\nCompleted 41.2 KiB/805.0 KiB (374.4 KiB/s) with 13 file(s) remaining\rCompleted 64.0 KiB/805.0 KiB (490.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000440-biopax2.owl to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440-biopax2.owl\nCompleted 64.0 KiB/805.0 KiB (490.3 KiB/s) with 12 file(s) remaining\rCompleted 73.2 KiB/805.0 KiB (551.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000440.m to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.m\nCompleted 73.2 KiB/805.0 KiB (551.9 KiB/s) with 11 file(s) remaining\rCompleted 88.1 KiB/805.0 KiB (638.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000440_url.sedml to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440_url.sedml\nCompleted 88.1 KiB/805.0 KiB (638.4 KiB/s) with 10 file(s) remaining\rCompleted 94.7 KiB/805.0 KiB (654.1 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/metadata.rdf\nCompleted 94.7 KiB/805.0 KiB (654.1 KiB/s) with 9 file(s) remaining\rCompleted 350.7 KiB/805.0 KiB (2.3 MiB/s) with 9 file(s) remaining \rCompleted 405.9 KiB/805.0 KiB (2.6 MiB/s) with 9 file(s) remaining \rupload: contents/BIOMD0000000440.vcml to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.vcml\nCompleted 405.9 KiB/805.0 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 442.6 KiB/805.0 KiB (2.7 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/curation_image.png\nCompleted 442.6 KiB/805.0 KiB (2.7 MiB/s) with 7 file(s) remaining\rCompleted 442.8 KiB/805.0 KiB (2.6 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/curation_notes.txt\nCompleted 442.8 KiB/805.0 KiB (2.6 MiB/s) with 6 file(s) remaining\rCompleted 497.6 KiB/805.0 KiB (2.8 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000440_url.xml to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440_url.xml\nCompleted 497.6 KiB/805.0 KiB (2.8 MiB/s) with 5 file(s) remaining\rCompleted 499.3 KiB/805.0 KiB (2.7 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/manifest.xml\nCompleted 499.3 KiB/805.0 KiB (2.7 MiB/s) with 4 file(s) remaining\rCompleted 528.1 KiB/805.0 KiB (2.5 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000440.png to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.png\nCompleted 528.1 KiB/805.0 KiB (2.5 MiB/s) with 3 file(s) remaining\rCompleted 571.7 KiB/805.0 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000440.svg to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.svg\nCompleted 571.7 KiB/805.0 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 578.6 KiB/805.0 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000440.ode to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.ode\nCompleted 578.6 KiB/805.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 805.0 KiB/805.0 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000440.pdf to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/contents/BIOMD0000000440.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (141.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cb40dcacb55678be5ce/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000440_url.sedml\ncreating dataset /BIOMD0000000440_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-43cc3748-6818d914-0c77-e45ea6-aba0ba, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000440_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-43cc3748-6818d914-fc3d-9b83a5-922994, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000440_url.sedml\ncreating attribute uri in /BIOMD0000000440_url.sedml\ncreating attribute _type in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000440_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000440_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000440_url.sedml\ncreate_links: /BIOMD0000000440_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000440_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000440_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000440_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000440_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000440_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000440_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000440_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000440_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710cb40dcacb55678be5ce\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 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 and upload the outputs of the simulation run ... 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":1.343462,"sedDocuments":[{"location":"BIOMD0000000440_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  BIOMD0000000440_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000440_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":0.927856,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.140165,"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":0.184912,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_0","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_5","status":"SUCCEEDED"},{"id":"autogen_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","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_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.456961,"curves":[{"id":"autogen_curve_task1_species_0","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_5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_10","status":"SUCCEEDED"}]}]}]}