{"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    455      0 --:--:-- --:--:-- --:--:--   457\n\r100  649k  100  649k    0     0  1470k      0 --:--:-- --:--:-- --:--:-- 1470k\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 (7.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (53.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/BIOMD0000000442_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000442_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 255.5 KiB/255.5 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/outputs/reports.h5\nCompleted 241.9 KiB/261.9 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/output.zip\nCompleted 241.9 KiB/261.9 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 244.5 KiB/261.9 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/rawLog.txt\nCompleted 244.5 KiB/261.9 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 251.6 KiB/261.9 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/outputs/plots.zip\nCompleted 251.6 KiB/261.9 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 261.9 KiB/261.9 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000442_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/outputs/BIOMD0000000442_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/BIOMD0000000442-biopax2.owl  \n  inflating: contents/BIOMD0000000442-biopax3.owl  \n  inflating: contents/BIOMD0000000442-matlab.m  \n  inflating: contents/BIOMD0000000442.m  \n  inflating: contents/BIOMD0000000442.ode  \n  inflating: contents/BIOMD0000000442.pdf  \n  inflating: contents/BIOMD0000000442.png  \n  inflating: contents/BIOMD0000000442.svg  \n  inflating: contents/BIOMD0000000442.vcml  \n  inflating: contents/BIOMD0000000442_url.sedml  \n  inflating: contents/BIOMD0000000442_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 38.1 KiB/1.0 MiB (500.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000442-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442-biopax3.owl\nCompleted 38.1 KiB/1.0 MiB (500.7 KiB/s) with 14 file(s) remaining\rCompleted 48.4 KiB/1.0 MiB (367.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000442.m to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.m\nCompleted 48.4 KiB/1.0 MiB (367.9 KiB/s) with 13 file(s) remaining\rCompleted 75.5 KiB/1.0 MiB (565.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000442-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442-biopax2.owl\nCompleted 75.5 KiB/1.0 MiB (565.1 KiB/s) with 12 file(s) remaining\rCompleted 139.2 KiB/1.0 MiB (1000.3 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000442.vcml to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.vcml\nCompleted 139.2 KiB/1.0 MiB (1000.3 KiB/s) with 11 file(s) remaining\rCompleted 145.7 KiB/1.0 MiB (1.0 MiB/s) with 11 file(s) remaining   \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/metadata.rdf\nCompleted 145.7 KiB/1.0 MiB (1.0 MiB/s) with 10 file(s) remaining\rCompleted 156.1 KiB/1.0 MiB (1.1 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000442-matlab.m to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442-matlab.m\nCompleted 156.1 KiB/1.0 MiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 173.5 KiB/1.0 MiB (973.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000442_url.sedml to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442_url.sedml\nCompleted 173.5 KiB/1.0 MiB (973.7 KiB/s) with 8 file(s) remaining\rCompleted 240.1 KiB/1.0 MiB (1.3 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000442_url.xml to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442_url.xml\nCompleted 240.1 KiB/1.0 MiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 496.1 KiB/1.0 MiB (2.7 MiB/s) with 7 file(s) remaining\rCompleted 497.8 KiB/1.0 MiB (2.6 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/manifest.xml\nCompleted 497.8 KiB/1.0 MiB (2.6 MiB/s) with 6 file(s) remaining\rCompleted 533.8 KiB/1.0 MiB (2.6 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/curation_image.png\nCompleted 533.8 KiB/1.0 MiB (2.6 MiB/s) with 5 file(s) remaining\rCompleted 534.0 KiB/1.0 MiB (2.6 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/curation_notes.txt\nCompleted 534.0 KiB/1.0 MiB (2.6 MiB/s) with 4 file(s) remaining\rCompleted 593.4 KiB/1.0 MiB (2.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000442.svg to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.svg\nCompleted 593.4 KiB/1.0 MiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 601.3 KiB/1.0 MiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000442.ode to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.ode\nCompleted 601.3 KiB/1.0 MiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 852.3 KiB/1.0 MiB (3.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000442.pdf to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.pdf\nCompleted 852.3 KiB/1.0 MiB (3.6 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (3.9 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000442.png to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/contents/BIOMD0000000442.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (112.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3377b6669655060da5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000442_url.sedml\ncreating dataset /BIOMD0000000442_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-cc6c195c-0082aeb4-cb9c-88d24b-bdcb3f, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000442_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-cc6c195c-0082aeb4-19f5-d15265-e5f291, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000442_url.sedml\ncreating attribute uri in /BIOMD0000000442_url.sedml\ncreating attribute _type in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000442_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000442_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000442_url.sedml\ncreate_links: /BIOMD0000000442_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000442_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000442_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000442_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000442_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000442_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000442_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000442_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000442_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b3377b6669655060da5\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.535378,"sedDocuments":[{"location":"BIOMD0000000442_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  BIOMD0000000442_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000442_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":1.139418,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.185972,"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":0.246126,"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_species_11","status":"SUCCEEDED"},{"id":"autogen_task1_species_12","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_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.565655,"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"},{"id":"autogen_curve_task1_species_11","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_12","status":"SUCCEEDED"}]}]}]}