{"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    433      0 --:--:-- --:--:-- --:--:--   434\n\r100  210k  100  210k    0     0   477k      0 --:--:-- --:--:-- --:--:--  477k\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 (20.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/rawLog.txt\nCompleted 2.7 KiB/2.7 KiB (36.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000435_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000435_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 21%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 119.7 KiB/119.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/outputs/reports.h5\nCompleted 103.8 KiB/123.7 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/output.zip\nCompleted 103.8 KiB/123.7 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 110.8 KiB/123.7 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/outputs/plots.zip\nCompleted 110.8 KiB/123.7 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 121.1 KiB/123.7 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000435_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/outputs/BIOMD0000000435_url.sedml/autogen_plot_for_task1.pdf\nCompleted 121.1 KiB/123.7 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 123.7 KiB/123.7 KiB (896.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000435-biopax2.owl  \n  inflating: contents/BIOMD0000000435-biopax3.owl  \n  inflating: contents/BIOMD0000000435-matlab.m  \n  inflating: contents/BIOMD0000000435-octave.m  \n  inflating: contents/BIOMD0000000435.m  \n  inflating: contents/BIOMD0000000435.ode  \n  inflating: contents/BIOMD0000000435.pdf  \n  inflating: contents/BIOMD0000000435.png  \n  inflating: contents/BIOMD0000000435.svg  \n  inflating: contents/BIOMD0000000435.vcml  \n  inflating: contents/BIOMD0000000435_url.sedml  \n  inflating: contents/BIOMD0000000435_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 11.9 KiB/406.3 KiB (159.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000435-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435-biopax2.owl\nCompleted 11.9 KiB/406.3 KiB (159.3 KiB/s) with 15 file(s) remaining\rCompleted 17.5 KiB/406.3 KiB (131.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000435-octave.m to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435-octave.m\nCompleted 17.5 KiB/406.3 KiB (131.7 KiB/s) with 14 file(s) remaining\rCompleted 74.9 KiB/406.3 KiB (534.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000435.png to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.png\nCompleted 74.9 KiB/406.3 KiB (534.3 KiB/s) with 13 file(s) remaining\rCompleted 80.4 KiB/406.3 KiB (564.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000435-matlab.m to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435-matlab.m\nCompleted 80.4 KiB/406.3 KiB (564.4 KiB/s) with 12 file(s) remaining\rCompleted 89.5 KiB/406.3 KiB (557.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000435_url.sedml to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435_url.sedml\nCompleted 89.5 KiB/406.3 KiB (557.9 KiB/s) with 11 file(s) remaining\rCompleted 133.9 KiB/406.3 KiB (794.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000435.vcml to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.vcml\nCompleted 133.9 KiB/406.3 KiB (794.9 KiB/s) with 10 file(s) remaining\rCompleted 135.7 KiB/406.3 KiB (795.9 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/manifest.xml\nCompleted 135.7 KiB/406.3 KiB (795.9 KiB/s) with 9 file(s) remaining\rCompleted 169.2 KiB/406.3 KiB (980.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000435_url.xml to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435_url.xml\nCompleted 169.2 KiB/406.3 KiB (980.5 KiB/s) with 8 file(s) remaining\rCompleted 169.6 KiB/406.3 KiB (946.4 KiB/s) with 8 file(s) remaining\rCompleted 181.3 KiB/406.3 KiB (1003.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/curation_image.png\nCompleted 181.3 KiB/406.3 KiB (1003.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/curation_notes.txt\nCompleted 181.3 KiB/406.3 KiB (1003.4 KiB/s) with 6 file(s) remaining\rCompleted 186.3 KiB/406.3 KiB (875.3 KiB/s) with 6 file(s) remaining \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/metadata.rdf\nCompleted 186.3 KiB/406.3 KiB (875.3 KiB/s) with 5 file(s) remaining\rCompleted 202.3 KiB/406.3 KiB (930.2 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000435-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435-biopax3.owl\nCompleted 202.3 KiB/406.3 KiB (930.2 KiB/s) with 4 file(s) remaining\rCompleted 373.2 KiB/406.3 KiB (1.6 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000435.pdf to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.pdf\nCompleted 373.2 KiB/406.3 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 376.5 KiB/406.3 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000435.ode to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.ode\nCompleted 376.5 KiB/406.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 382.1 KiB/406.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000435.m to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.m\nCompleted 382.1 KiB/406.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 406.3 KiB/406.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000435.svg to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/contents/BIOMD0000000435.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (117.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2e0fb37cdb9ae7321d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000435_url.sedml\ncreating dataset /BIOMD0000000435_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-13a982a7-6d9f8f9d-eb7e-982d39-140ca6, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000435_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-13a982a7-6d9f8f9d-ab4a-99d2be-962714, chunk_size: (14, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000435_url.sedml\ncreating attribute uri in /BIOMD0000000435_url.sedml\ncreating attribute _type in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000435_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000435_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000435_url.sedml\ncreate_links: /BIOMD0000000435_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000435_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000435_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000435_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000435_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000435_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000435_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000435_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000435_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b2e0fb37cdb9ae7321d\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 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.\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":1.27567,"sedDocuments":[{"location":"BIOMD0000000435_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  BIOMD0000000435_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 14 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000435_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":0.889366,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.151333,"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":0.188107,"dataSets":[{"id":"autogen_time_for_task1","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_compartment_1","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.426785,"curves":[{"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"}]}]}]}