{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r100  301k  100  301k    0     0   706k      0 --:--:-- --:--:-- --:--:--  706k\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 (22.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (49.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000221_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000221_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 146.3 KiB/146.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/outputs/reports.h5\nCompleted 135.2 KiB/160.5 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/output.zip\nCompleted 135.2 KiB/160.5 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 144.7 KiB/160.5 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/outputs/plots.zip\nCompleted 144.7 KiB/160.5 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 157.9 KiB/160.5 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000221_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/outputs/BIOMD0000000221_url.sedml/autogen_plot_for_task1.pdf\nCompleted 157.9 KiB/160.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 160.5 KiB/160.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000221-biopax2.owl  \n  inflating: contents/BIOMD0000000221-biopax3.owl  \n  inflating: contents/BIOMD0000000221-matlab.m  \n  inflating: contents/BIOMD0000000221-octave.m  \n  inflating: contents/BIOMD0000000221.m  \n  inflating: contents/BIOMD0000000221.ode  \n  inflating: contents/BIOMD0000000221.pdf  \n  inflating: contents/BIOMD0000000221.png  \n  inflating: contents/BIOMD0000000221.svg  \n  inflating: contents/BIOMD0000000221.vcml  \n  inflating: contents/BIOMD0000000221_manual.png  \n  inflating: contents/BIOMD0000000221_manual.svg  \n  inflating: contents/BIOMD0000000221_url.sedml  \n  inflating: contents/BIOMD0000000221_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 37.7 KiB/617.1 KiB (472.5 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000221-biopax3.owl to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221-biopax3.owl\nCompleted 37.7 KiB/617.1 KiB (472.5 KiB/s) with 17 file(s) remaining\rCompleted 48.3 KiB/617.1 KiB (487.2 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000221-matlab.m to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221-matlab.m\nCompleted 48.3 KiB/617.1 KiB (487.2 KiB/s) with 16 file(s) remaining\rCompleted 58.9 KiB/617.1 KiB (459.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000221-octave.m to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221-octave.m\nCompleted 58.9 KiB/617.1 KiB (459.3 KiB/s) with 15 file(s) remaining\rCompleted 89.5 KiB/617.1 KiB (661.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000221.svg to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.svg\nCompleted 89.5 KiB/617.1 KiB (661.2 KiB/s) with 14 file(s) remaining\rCompleted 116.6 KiB/617.1 KiB (850.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000221-biopax2.owl to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221-biopax2.owl\nCompleted 116.6 KiB/617.1 KiB (850.8 KiB/s) with 13 file(s) remaining\rCompleted 163.2 KiB/617.1 KiB (1.1 MiB/s) with 13 file(s) remaining  \rupload: contents/BIOMD0000000221_url.xml to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221_url.xml\nCompleted 163.2 KiB/617.1 KiB (1.1 MiB/s) with 12 file(s) remaining\rCompleted 163.5 KiB/617.1 KiB (1.0 MiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/curation_notes.txt\nCompleted 163.5 KiB/617.1 KiB (1.0 MiB/s) with 11 file(s) remaining\rCompleted 213.8 KiB/617.1 KiB (1.3 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000221.vcml to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.vcml\nCompleted 213.8 KiB/617.1 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 229.2 KiB/617.1 KiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000221_manual.png to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221_manual.png\nCompleted 229.2 KiB/617.1 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 231.3 KiB/617.1 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/manifest.xml\nCompleted 231.3 KiB/617.1 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 246.1 KiB/617.1 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000221_url.sedml to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221_url.sedml\nCompleted 246.1 KiB/617.1 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 276.7 KiB/617.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 292.1 KiB/617.1 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000221.png to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.png\nCompleted 292.1 KiB/617.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 297.4 KiB/617.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/metadata.rdf\nCompleted 297.4 KiB/617.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000221_manual.svg to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221_manual.svg\nCompleted 297.4 KiB/617.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 308.0 KiB/617.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000221.m to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.m\nCompleted 308.0 KiB/617.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 315.0 KiB/617.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000221.ode to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.ode\nCompleted 315.0 KiB/617.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 512.8 KiB/617.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000221.pdf to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/BIOMD0000000221.pdf\nCompleted 512.8 KiB/617.1 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 617.1 KiB/617.1 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (148.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109cc9a62a8be53f78973/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000221_url.sedml\ncreating dataset /BIOMD0000000221_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-06270f6a-f43c2cc8-59e0-253709-de8683, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000221_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\ndataset created, uuid: d-06270f6a-f43c2cc8-5ef9-00a752-4dc386, chunk_size: (25, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000221_url.sedml\ncreating attribute uri in /BIOMD0000000221_url.sedml\ncreating attribute _type in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000221_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000221_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000221_url.sedml\ncreate_links: /BIOMD0000000221_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000221_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000221_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000221_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000221_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000221_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000221_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\niterating over chunks for /BIOMD0000000221_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000221_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109cc9a62a8be53f78973\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 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.\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":1.600221,"sedDocuments":[{"location":"BIOMD0000000221_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  BIOMD0000000221_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000221_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":1.150907,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.2015,"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":0.235242,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_aca","status":"SUCCEEDED"},{"id":"autogen_task1_oaa","status":"SUCCEEDED"},{"id":"autogen_task1_coa","status":"SUCCEEDED"},{"id":"autogen_task1_cit","status":"SUCCEEDED"},{"id":"autogen_task1_icit","status":"SUCCEEDED"},{"id":"autogen_task1_akg","status":"SUCCEEDED"},{"id":"autogen_task1_sca","status":"SUCCEEDED"},{"id":"autogen_task1_suc","status":"SUCCEEDED"},{"id":"autogen_task1_fa","status":"SUCCEEDED"},{"id":"autogen_task1_mal","status":"SUCCEEDED"},{"id":"autogen_task1_gly","status":"SUCCEEDED"},{"id":"autogen_task1_biosyn","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_CS","status":"SUCCEEDED"},{"id":"autogen_task1_ACN","status":"SUCCEEDED"},{"id":"autogen_task1_ICD","status":"SUCCEEDED"},{"id":"autogen_task1_KDH","status":"SUCCEEDED"},{"id":"autogen_task1_ScAS","status":"SUCCEEDED"},{"id":"autogen_task1_SDH","status":"SUCCEEDED"},{"id":"autogen_task1_FUM","status":"SUCCEEDED"},{"id":"autogen_task1_MDH","status":"SUCCEEDED"},{"id":"autogen_task1_ICL","status":"SUCCEEDED"},{"id":"autogen_task1_MS","status":"SUCCEEDED"},{"id":"autogen_task1_SYN","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.561397,"curves":[{"id":"autogen_curve_task1_aca","status":"SUCCEEDED"},{"id":"autogen_curve_task1_oaa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_icit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_akg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_sca","status":"SUCCEEDED"},{"id":"autogen_curve_task1_suc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_fa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mal","status":"SUCCEEDED"},{"id":"autogen_curve_task1_gly","status":"SUCCEEDED"},{"id":"autogen_curve_task1_biosyn","status":"SUCCEEDED"}]}]}]}