{"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    463      0 --:--:-- --:--:-- --:--:--   464\n\r 63  190k   63  121k    0     0   304k      0 --:--:-- --:--:-- --:--:--  304k\r100  190k  100  190k    0     0   474k      0 --:--:-- --:--:-- --:--:-- 22.5M\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 (18.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (41.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/BIOMD0000000485_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000485_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 31%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 68.9 KiB/68.9 KiB (623.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/outputs/reports.h5\nCompleted 56.2 KiB/74.9 KiB (717.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/output.zip\nCompleted 56.2 KiB/74.9 KiB (717.9 KiB/s) with 3 file(s) remaining\rCompleted 62.7 KiB/74.9 KiB (599.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/outputs/plots.zip\nCompleted 62.7 KiB/74.9 KiB (599.6 KiB/s) with 2 file(s) remaining\rCompleted 72.2 KiB/74.9 KiB (654.1 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000485_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/outputs/BIOMD0000000485_url.sedml/autogen_plot_for_task1.pdf\nCompleted 72.2 KiB/74.9 KiB (654.1 KiB/s) with 1 file(s) remaining\rCompleted 74.9 KiB/74.9 KiB (652.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000485-biopax2.owl  \n  inflating: contents/BIOMD0000000485-biopax3.owl  \n  inflating: contents/BIOMD0000000485-matlab.m  \n  inflating: contents/BIOMD0000000485-octave.m  \n  inflating: contents/BIOMD0000000485.m  \n  inflating: contents/BIOMD0000000485.ode  \n  inflating: contents/BIOMD0000000485.pdf  \n  inflating: contents/BIOMD0000000485.png  \n  inflating: contents/BIOMD0000000485.sci  \n  inflating: contents/BIOMD0000000485.svg  \n  inflating: contents/BIOMD0000000485.vcml  \n  inflating: contents/BIOMD0000000485_url.sedml  \n  inflating: contents/BIOMD0000000485_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 11.4 KiB/291.9 KiB (156.4 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000485-biopax3.owl to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485-biopax3.owl\nCompleted 11.4 KiB/291.9 KiB (156.4 KiB/s) with 16 file(s) remaining\rCompleted 14.9 KiB/291.9 KiB (147.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000485-matlab.m to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485-matlab.m\nCompleted 14.9 KiB/291.9 KiB (147.0 KiB/s) with 15 file(s) remaining\rCompleted 15.5 KiB/291.9 KiB (117.9 KiB/s) with 15 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/curation_notes.txt\nCompleted 15.5 KiB/291.9 KiB (117.9 KiB/s) with 14 file(s) remaining\rCompleted 19.0 KiB/291.9 KiB (134.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000485-octave.m to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485-octave.m\nCompleted 19.0 KiB/291.9 KiB (134.1 KiB/s) with 13 file(s) remaining\rCompleted 27.1 KiB/291.9 KiB (187.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000485-biopax2.owl to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485-biopax2.owl\nCompleted 27.1 KiB/291.9 KiB (187.8 KiB/s) with 12 file(s) remaining\rCompleted 28.5 KiB/291.9 KiB (190.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000485.sci to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.sci\nCompleted 28.5 KiB/291.9 KiB (190.7 KiB/s) with 11 file(s) remaining\rCompleted 39.4 KiB/291.9 KiB (252.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000485.svg to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.svg\nCompleted 39.4 KiB/291.9 KiB (252.1 KiB/s) with 10 file(s) remaining\rCompleted 41.4 KiB/291.9 KiB (258.0 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/manifest.xml\nCompleted 41.4 KiB/291.9 KiB (258.0 KiB/s) with 9 file(s) remaining\rCompleted 50.5 KiB/291.9 KiB (308.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000485_url.sedml to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485_url.sedml\nCompleted 50.5 KiB/291.9 KiB (308.5 KiB/s) with 8 file(s) remaining\rCompleted 58.9 KiB/291.9 KiB (356.5 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000485_url.xml to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485_url.xml\nCompleted 58.9 KiB/291.9 KiB (356.5 KiB/s) with 7 file(s) remaining\rCompleted 60.6 KiB/291.9 KiB (294.8 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/metadata.rdf\nCompleted 60.6 KiB/291.9 KiB (294.8 KiB/s) with 6 file(s) remaining\rCompleted 86.6 KiB/291.9 KiB (417.6 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/curation_image.png\nCompleted 86.6 KiB/291.9 KiB (417.6 KiB/s) with 5 file(s) remaining\rCompleted 88.3 KiB/291.9 KiB (415.5 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000485.ode to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.ode\nCompleted 88.3 KiB/291.9 KiB (415.5 KiB/s) with 4 file(s) remaining\rCompleted 101.1 KiB/291.9 KiB (467.2 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000485.vcml to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.vcml\nCompleted 101.1 KiB/291.9 KiB (467.2 KiB/s) with 3 file(s) remaining\rCompleted 104.6 KiB/291.9 KiB (474.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000485.m to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.m\nCompleted 104.6 KiB/291.9 KiB (474.5 KiB/s) with 2 file(s) remaining\rCompleted 144.0 KiB/291.9 KiB (638.1 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000485.png to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.png\nCompleted 144.0 KiB/291.9 KiB (638.1 KiB/s) with 1 file(s) remaining\rCompleted 291.9 KiB/291.9 KiB (1.2 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000485.pdf to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/contents/BIOMD0000000485.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (132.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d719a62a8be53f80de2/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000485_url.sedml\ncreating dataset /BIOMD0000000485_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-d6684531-666d0b89-4b3b-1f1e22-7cf990, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000485_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-d6684531-666d0b89-b840-c5cd4f-81ea0c, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000485_url.sedml\ncreating attribute uri in /BIOMD0000000485_url.sedml\ncreating attribute _type in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000485_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000485_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000485_url.sedml\ncreate_links: /BIOMD0000000485_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000485_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000485_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000485_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000485_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000485_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000485_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /BIOMD0000000485_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000485_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710d719a62a8be53f80de2\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\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":15.879352,"sedDocuments":[{"location":"BIOMD0000000485_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  BIOMD0000000485_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000485_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":15.572079,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":15.106274,"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":0.151318,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_ES","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_value","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.203451,"curves":[{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ES","status":"SUCCEEDED"}]}]}]}