{"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    439      0 --:--:-- --:--:-- --:--:--   439\n\r100  304k  100  304k    0     0   692k      0 --:--:-- --:--:-- --:--:--  692k\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 (23.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (58.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/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/BIOMD0000000229_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000229_url.sedml/autogen_plot_for_task1.pdf (deflated 22%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 235.4 KiB/235.4 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/outputs/reports.h5\nCompleted 222.5 KiB/254.0 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/output.zip\nCompleted 222.5 KiB/254.0 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 235.0 KiB/254.0 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/outputs/plots.zip\nCompleted 235.0 KiB/254.0 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 237.7 KiB/254.0 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/rawLog.txt\nCompleted 237.7 KiB/254.0 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 254.0 KiB/254.0 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000229_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/outputs/BIOMD0000000229_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/BIOMD0000000229-biopax2.owl  \n  inflating: contents/BIOMD0000000229-biopax3.owl  \n  inflating: contents/BIOMD0000000229-matlab.m  \n  inflating: contents/BIOMD0000000229-octave.m  \n  inflating: contents/BIOMD0000000229.m  \n  inflating: contents/BIOMD0000000229.ode  \n  inflating: contents/BIOMD0000000229.pdf  \n  inflating: contents/BIOMD0000000229.png  \n  inflating: contents/BIOMD0000000229.sci  \n  inflating: contents/BIOMD0000000229.svg  \n  inflating: contents/BIOMD0000000229.vcml  \n  inflating: contents/BIOMD0000000229_url.sedml  \n  inflating: contents/BIOMD0000000229_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 23.8 KiB/523.5 KiB (220.7 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000229-biopax3.owl to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229-biopax3.owl\nCompleted 23.8 KiB/523.5 KiB (220.7 KiB/s) with 16 file(s) remaining\rCompleted 28.8 KiB/523.5 KiB (217.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000229-matlab.m to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229-matlab.m\nCompleted 28.8 KiB/523.5 KiB (217.6 KiB/s) with 15 file(s) remaining\rCompleted 33.7 KiB/523.5 KiB (244.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000229-octave.m to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229-octave.m\nCompleted 33.7 KiB/523.5 KiB (244.9 KiB/s) with 14 file(s) remaining\rCompleted 51.1 KiB/523.5 KiB (355.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000229-biopax2.owl to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229-biopax2.owl\nCompleted 51.1 KiB/523.5 KiB (355.0 KiB/s) with 13 file(s) remaining\rCompleted 53.2 KiB/523.5 KiB (364.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000229.sci to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.sci\nCompleted 53.2 KiB/523.5 KiB (364.7 KiB/s) with 12 file(s) remaining\rCompleted 83.9 KiB/523.5 KiB (567.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000229.svg to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.svg\nCompleted 83.9 KiB/523.5 KiB (567.8 KiB/s) with 11 file(s) remaining\rCompleted 103.6 KiB/523.5 KiB (661.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000229_url.sedml to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229_url.sedml\nCompleted 103.6 KiB/523.5 KiB (661.0 KiB/s) with 10 file(s) remaining\rCompleted 144.3 KiB/523.5 KiB (900.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000229.vcml to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.vcml\nCompleted 144.3 KiB/523.5 KiB (900.0 KiB/s) with 9 file(s) remaining\rCompleted 144.5 KiB/523.5 KiB (842.1 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/curation_notes.txt\nCompleted 144.5 KiB/523.5 KiB (842.1 KiB/s) with 8 file(s) remaining\rCompleted 169.9 KiB/523.5 KiB (906.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000229_url.xml to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229_url.xml\nCompleted 169.9 KiB/523.5 KiB (906.8 KiB/s) with 7 file(s) remaining\rCompleted 171.8 KiB/523.5 KiB (881.2 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/manifest.xml\nCompleted 171.8 KiB/523.5 KiB (881.2 KiB/s) with 6 file(s) remaining\rCompleted 250.1 KiB/523.5 KiB (1.2 MiB/s) with 6 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/curation_image.png\nCompleted 250.1 KiB/523.5 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 253.1 KiB/523.5 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000229.ode to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.ode\nCompleted 253.1 KiB/523.5 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 258.1 KiB/523.5 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000229.m to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.m\nCompleted 258.1 KiB/523.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 262.9 KiB/523.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/metadata.rdf\nCompleted 262.9 KiB/523.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 337.7 KiB/523.5 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000229.png to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.png\nCompleted 337.7 KiB/523.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 523.5 KiB/523.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000229.pdf to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/contents/BIOMD0000000229.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (128.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109eb9a62a8be53f78ce8/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000229_url.sedml\ncreating dataset /BIOMD0000000229_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-174f4d34-13df0c5a-2847-ba2e19-b59720, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000229_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\ndataset created, uuid: d-174f4d34-13df0c5a-e28d-424e89-d6960e, chunk_size: (37, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000229_url.sedml\ncreating attribute uri in /BIOMD0000000229_url.sedml\ncreating attribute _type in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000229_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000229_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000229_url.sedml\ncreate_links: /BIOMD0000000229_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000229_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000229_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000229_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000229_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000229_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000229_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\niterating over chunks for /BIOMD0000000229_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 37, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000229_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109eb9a62a8be53f78ce8\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":16.396632,"sedDocuments":[{"location":"BIOMD0000000229_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  BIOMD0000000229_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000229_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":16.082873,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":15.346891,"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":0.30093,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_ACA","status":"SUCCEEDED"},{"id":"autogen_task1_CAR1","status":"SUCCEEDED"},{"id":"autogen_task1_PKA","status":"SUCCEEDED"},{"id":"autogen_task1_incAMP","status":"SUCCEEDED"},{"id":"autogen_task1_ERK2","status":"SUCCEEDED"},{"id":"autogen_task1_REGA","status":"SUCCEEDED"},{"id":"autogen_task1_excAMP","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_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","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_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v13","status":"SUCCEEDED"},{"id":"autogen_task1_v14","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.310298,"curves":[{"id":"autogen_curve_task1_ACA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CAR1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PKA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_incAMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ERK2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_REGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_excAMP","status":"SUCCEEDED"}]}]}]}