{"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    464      0 --:--:-- --:--:-- --:--:--   463\n\r100  192k  100  192k    0     0   464k      0 --:--:-- --:--:-- --:--:--  464k\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 (25.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/rawLog.txt\nCompleted 3.0 KiB/3.0 KiB (45.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/BIOMD0000000084_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000084_url.sedml/autogen_plot_for_task1.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 172.6 KiB/172.6 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/outputs/reports.h5\nCompleted 8.5 KiB/185.3 KiB (91.7 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/outputs/plots.zip\nCompleted 8.5 KiB/185.3 KiB (91.7 KiB/s) with 3 file(s) remaining\rCompleted 20.1 KiB/185.3 KiB (151.4 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000084_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/outputs/BIOMD0000000084_url.sedml/autogen_plot_for_task1.pdf\nCompleted 20.1 KiB/185.3 KiB (151.4 KiB/s) with 2 file(s) remaining\rCompleted 182.7 KiB/185.3 KiB (1.2 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/output.zip\nCompleted 182.7 KiB/185.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 185.3 KiB/185.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000084-biopax2.owl  \n  inflating: contents/BIOMD0000000084-biopax3.owl  \n  inflating: contents/BIOMD0000000084-matlab.m  \n  inflating: contents/BIOMD0000000084-octave.m  \n  inflating: contents/BIOMD0000000084.m  \n  inflating: contents/BIOMD0000000084.ode  \n  inflating: contents/BIOMD0000000084.pdf  \n  inflating: contents/BIOMD0000000084.png  \n  inflating: contents/BIOMD0000000084.sci  \n  inflating: contents/BIOMD0000000084.svg  \n  inflating: contents/BIOMD0000000084.vcml  \n  inflating: contents/BIOMD0000000084_url.sedml  \n  inflating: contents/BIOMD0000000084_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 23.7 KiB/375.3 KiB (323.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000084-biopax3.owl to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084-biopax3.owl\nCompleted 23.7 KiB/375.3 KiB (323.6 KiB/s) with 16 file(s) remaining\rCompleted 28.8 KiB/375.3 KiB (232.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000084-matlab.m to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084-matlab.m\nCompleted 28.8 KiB/375.3 KiB (232.1 KiB/s) with 15 file(s) remaining\rCompleted 28.9 KiB/375.3 KiB (224.7 KiB/s) with 15 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/curation_notes.txt\nCompleted 28.9 KiB/375.3 KiB (224.7 KiB/s) with 14 file(s) remaining\rCompleted 34.1 KiB/375.3 KiB (261.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000084-octave.m to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084-octave.m\nCompleted 34.1 KiB/375.3 KiB (261.2 KiB/s) with 13 file(s) remaining\rCompleted 37.1 KiB/375.3 KiB (281.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000084.sci to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.sci\nCompleted 37.1 KiB/375.3 KiB (281.3 KiB/s) with 12 file(s) remaining\rCompleted 48.0 KiB/375.3 KiB (330.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000084_url.sedml to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084_url.sedml\nCompleted 48.0 KiB/375.3 KiB (330.0 KiB/s) with 11 file(s) remaining\rCompleted 87.7 KiB/375.3 KiB (587.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000084.png to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.png\nCompleted 87.7 KiB/375.3 KiB (587.3 KiB/s) with 10 file(s) remaining\rCompleted 117.4 KiB/375.3 KiB (760.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000084.vcml to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.vcml\nCompleted 117.4 KiB/375.3 KiB (760.8 KiB/s) with 9 file(s) remaining\rCompleted 138.5 KiB/375.3 KiB (884.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000084.svg to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.svg\nCompleted 138.5 KiB/375.3 KiB (884.9 KiB/s) with 8 file(s) remaining\rCompleted 159.9 KiB/375.3 KiB (953.2 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000084_url.xml to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084_url.xml\nCompleted 159.9 KiB/375.3 KiB (953.2 KiB/s) with 7 file(s) remaining\rCompleted 161.9 KiB/375.3 KiB (849.0 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/manifest.xml\nCompleted 161.9 KiB/375.3 KiB (849.0 KiB/s) with 6 file(s) remaining\rCompleted 179.0 KiB/375.3 KiB (911.4 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000084-biopax2.owl to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084-biopax2.owl\nCompleted 179.0 KiB/375.3 KiB (911.4 KiB/s) with 5 file(s) remaining\rCompleted 181.7 KiB/375.3 KiB (903.8 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/metadata.rdf\nCompleted 181.7 KiB/375.3 KiB (903.8 KiB/s) with 4 file(s) remaining\rCompleted 349.8 KiB/375.3 KiB (1.6 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000084.pdf to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.pdf\nCompleted 349.8 KiB/375.3 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 352.8 KiB/375.3 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000084.ode to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.ode\nCompleted 352.8 KiB/375.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 357.9 KiB/375.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000084.m to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/BIOMD0000000084.m\nCompleted 357.9 KiB/375.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 375.3 KiB/375.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/contents/curation_image.jpeg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (134.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108099a62a8be53f75178/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000084_url.sedml\ncreating dataset /BIOMD0000000084_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-f1cc2be2-c80357ec-9586-8955cb-10e16d, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000084_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-f1cc2be2-c80357ec-ce4b-5781e8-2219a7, chunk_size: (18, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000084_url.sedml\ncreating attribute uri in /BIOMD0000000084_url.sedml\ncreating attribute _type in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000084_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000084_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000084_url.sedml\ncreate_links: /BIOMD0000000084_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000084_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000084_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000084_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000084_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000084_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000084_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /BIOMD0000000084_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000084_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108099a62a8be53f75178\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 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.\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":17.197166,"sedDocuments":[{"location":"BIOMD0000000084_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  BIOMD0000000084_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 18 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000084_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":16.898188,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.277511,"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":0.174434,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_Rin","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x1p","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_x2p","status":"SUCCEEDED"},{"id":"autogen_task1_x3","status":"SUCCEEDED"},{"id":"autogen_task1_x3p","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.329809,"curves":[{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rin","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x1p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x3p","status":"SUCCEEDED"}]}]}]}