{"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    443      0 --:--:-- --:--:-- --:--:--   444\n\r100  183k  100  183k    0     0   412k      0 --:--:-- --:--:-- --:--:--  412k\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 (24.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (25.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/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/BIOMD0000000006_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000006_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 28%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 91.9 KiB/91.9 KiB (955.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/outputs/reports.h5\nCompleted 75.0 KiB/93.1 KiB (840.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/output.zip\nCompleted 75.0 KiB/93.1 KiB (840.5 KiB/s) with 3 file(s) remaining\rCompleted 81.1 KiB/93.1 KiB (759.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/outputs/plots.zip\nCompleted 81.1 KiB/93.1 KiB (759.4 KiB/s) with 2 file(s) remaining\rCompleted 90.5 KiB/93.1 KiB (797.5 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000006_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/outputs/BIOMD0000000006_url.sedml/autogen_plot_for_task1.pdf\nCompleted 90.5 KiB/93.1 KiB (797.5 KiB/s) with 1 file(s) remaining\rCompleted 93.1 KiB/93.1 KiB (715.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000006-biopax2.owl  \n  inflating: contents/BIOMD0000000006-biopax3.owl  \n  inflating: contents/BIOMD0000000006-matlab.m  \n  inflating: contents/BIOMD0000000006-octave.m  \n  inflating: contents/BIOMD0000000006.m  \n  inflating: contents/BIOMD0000000006.ode  \n  inflating: contents/BIOMD0000000006.pdf  \n  inflating: contents/BIOMD0000000006.png  \n  inflating: contents/BIOMD0000000006.sci  \n  inflating: contents/BIOMD0000000006.svg  \n  inflating: contents/BIOMD0000000006_manual.png  \n  inflating: contents/BIOMD0000000006_manual.svg  \n  inflating: contents/BIOMD0000000006_url.sedml  \n  inflating: contents/BIOMD0000000006_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 3.5 KiB/285.9 KiB (28.8 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000006-matlab.m to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006-matlab.m\nCompleted 3.5 KiB/285.9 KiB (28.8 KiB/s) with 17 file(s) remaining\rCompleted 6.9 KiB/285.9 KiB (47.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000006-octave.m to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006-octave.m\nCompleted 6.9 KiB/285.9 KiB (47.6 KiB/s) with 16 file(s) remaining\rCompleted 11.8 KiB/285.9 KiB (78.4 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000006_manual.png to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006_manual.png\nCompleted 11.8 KiB/285.9 KiB (78.4 KiB/s) with 15 file(s) remaining\rCompleted 20.1 KiB/285.9 KiB (118.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000006-biopax2.owl to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006-biopax2.owl\nCompleted 20.1 KiB/285.9 KiB (118.1 KiB/s) with 14 file(s) remaining\rCompleted 29.5 KiB/285.9 KiB (170.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000006_manual.svg to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006_manual.svg\nCompleted 29.5 KiB/285.9 KiB (170.3 KiB/s) with 13 file(s) remaining\rCompleted 30.5 KiB/285.9 KiB (169.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000006.sci to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.sci\nCompleted 30.5 KiB/285.9 KiB (169.5 KiB/s) with 12 file(s) remaining\rCompleted 39.9 KiB/285.9 KiB (215.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000006.svg to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.svg\nCompleted 39.9 KiB/285.9 KiB (215.5 KiB/s) with 11 file(s) remaining\rCompleted 48.4 KiB/285.9 KiB (255.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000006_url.sedml to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006_url.sedml\nCompleted 48.4 KiB/285.9 KiB (255.9 KiB/s) with 10 file(s) remaining\rCompleted 63.5 KiB/285.9 KiB (323.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000006_url.xml to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006_url.xml\nCompleted 63.5 KiB/285.9 KiB (323.0 KiB/s) with 9 file(s) remaining\rCompleted 74.5 KiB/285.9 KiB (371.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000006-biopax3.owl to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006-biopax3.owl\nCompleted 74.5 KiB/285.9 KiB (371.2 KiB/s) with 8 file(s) remaining\rCompleted 113.6 KiB/285.9 KiB (562.6 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/curation_image.png\nCompleted 113.6 KiB/285.9 KiB (562.6 KiB/s) with 7 file(s) remaining\rCompleted 114.3 KiB/285.9 KiB (521.0 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/curation_notes.txt\nCompleted 114.3 KiB/285.9 KiB (521.0 KiB/s) with 6 file(s) remaining\rCompleted 116.4 KiB/285.9 KiB (490.3 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/manifest.xml\nCompleted 116.4 KiB/285.9 KiB (490.3 KiB/s) with 5 file(s) remaining\rCompleted 119.8 KiB/285.9 KiB (496.9 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000006.m to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.m\nCompleted 119.8 KiB/285.9 KiB (496.9 KiB/s) with 4 file(s) remaining\rCompleted 125.7 KiB/285.9 KiB (474.9 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/metadata.rdf\nCompleted 125.7 KiB/285.9 KiB (474.9 KiB/s) with 3 file(s) remaining\rCompleted 279.3 KiB/285.9 KiB (1.0 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000006.pdf to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.pdf\nCompleted 279.3 KiB/285.9 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 281.0 KiB/285.9 KiB (1010.5 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000006.ode to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.ode\nCompleted 281.0 KiB/285.9 KiB (1010.5 KiB/s) with 1 file(s) remaining\rCompleted 285.9 KiB/285.9 KiB (789.8 KiB/s) with 1 file(s) remaining \rupload: contents/BIOMD0000000006.png to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/contents/BIOMD0000000006.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (130.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107010dcacb55678b361c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000006_url.sedml\ncreating dataset /BIOMD0000000006_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-f9889b3d-6c0c18ad-5d7d-22cd2f-e1026d, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000006_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-f9889b3d-6c0c18ad-843a-bef630-771134, chunk_size: (14, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000006_url.sedml\ncreating attribute uri in /BIOMD0000000006_url.sedml\ncreating attribute _type in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000006_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000006_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000006_url.sedml\ncreate_links: /BIOMD0000000006_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000006_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000006_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000006_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000006_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000006_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000006_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000006_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000006_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107010dcacb55678b361c\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 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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":21.456706,"sedDocuments":[{"location":"BIOMD0000000006_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  BIOMD0000000006_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: BIOMD0000000006_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":21.141116,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":20.598881,"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":0.167618,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k4prime","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.268794,"curves":[{"id":"autogen_curve_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_curve_task1_u","status":"SUCCEEDED"},{"id":"autogen_curve_task1_z","status":"SUCCEEDED"},{"id":"autogen_curve_task1_v","status":"SUCCEEDED"}]}]}]}