{"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    410      0 --:--:-- --:--:-- --:--:--   410\n\r100  207k  100  207k    0     0   457k      0 --:--:-- --:--:-- --:--:--  457k\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 (27.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (42.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000068_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000068_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 41%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 61.8 KiB/61.8 KiB (704.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/outputs/reports.h5\nCompleted 47.3 KiB/70.1 KiB (585.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/output.zip\nCompleted 47.3 KiB/70.1 KiB (585.9 KiB/s) with 3 file(s) remaining\rCompleted 55.3 KiB/70.1 KiB (424.8 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/outputs/plots.zip\nCompleted 55.3 KiB/70.1 KiB (424.8 KiB/s) with 2 file(s) remaining\rCompleted 67.4 KiB/70.1 KiB (453.6 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000068_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/outputs/BIOMD0000000068_url.sedml/autogen_plot_for_task1.pdf\nCompleted 67.4 KiB/70.1 KiB (453.6 KiB/s) with 1 file(s) remaining\rCompleted 70.1 KiB/70.1 KiB (462.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000068-biopax2.owl  \n  inflating: contents/BIOMD0000000068-biopax3.owl  \n  inflating: contents/BIOMD0000000068-matlab.m  \n  inflating: contents/BIOMD0000000068-octave.m  \n  inflating: contents/BIOMD0000000068.m  \n  inflating: contents/BIOMD0000000068.ode  \n  inflating: contents/BIOMD0000000068.pdf  \n  inflating: contents/BIOMD0000000068.png  \n  inflating: contents/BIOMD0000000068.svg  \n  inflating: contents/BIOMD0000000068.vcml  \n  inflating: contents/BIOMD0000000068_url.sedml  \n  inflating: contents/BIOMD0000000068_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 21.2 KiB/366.0 KiB (194.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000068-biopax3.owl to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068-biopax3.owl\nCompleted 21.2 KiB/366.0 KiB (194.5 KiB/s) with 15 file(s) remaining\rCompleted 32.7 KiB/366.0 KiB (256.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000068.svg to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.svg\nCompleted 32.7 KiB/366.0 KiB (256.7 KiB/s) with 14 file(s) remaining\rCompleted 37.2 KiB/366.0 KiB (279.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000068-matlab.m to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068-matlab.m\nCompleted 37.2 KiB/366.0 KiB (279.7 KiB/s) with 13 file(s) remaining\rCompleted 46.6 KiB/366.0 KiB (301.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000068_url.sedml to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068_url.sedml\nCompleted 46.6 KiB/366.0 KiB (301.1 KiB/s) with 12 file(s) remaining\rCompleted 63.5 KiB/366.0 KiB (405.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000068-biopax2.owl to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068-biopax2.owl\nCompleted 63.5 KiB/366.0 KiB (405.1 KiB/s) with 11 file(s) remaining\rCompleted 68.0 KiB/366.0 KiB (415.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000068-octave.m to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068-octave.m\nCompleted 68.0 KiB/366.0 KiB (415.5 KiB/s) with 10 file(s) remaining\rCompleted 69.8 KiB/366.0 KiB (404.6 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/manifest.xml\nCompleted 69.8 KiB/366.0 KiB (404.6 KiB/s) with 9 file(s) remaining\rCompleted 81.9 KiB/366.0 KiB (467.9 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/curation_image.png\nCompleted 81.9 KiB/366.0 KiB (467.9 KiB/s) with 8 file(s) remaining\rCompleted 112.9 KiB/366.0 KiB (617.6 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000068.vcml to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.vcml\nCompleted 112.9 KiB/366.0 KiB (617.6 KiB/s) with 7 file(s) remaining\rCompleted 118.9 KiB/366.0 KiB (616.7 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/metadata.rdf\nCompleted 118.9 KiB/366.0 KiB (616.7 KiB/s) with 6 file(s) remaining\rCompleted 119.0 KiB/366.0 KiB (580.3 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/curation_notes.txt\nCompleted 119.0 KiB/366.0 KiB (580.3 KiB/s) with 5 file(s) remaining\rCompleted 121.7 KiB/366.0 KiB (561.2 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000068.ode to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.ode\nCompleted 121.7 KiB/366.0 KiB (561.2 KiB/s) with 4 file(s) remaining\rCompleted 144.1 KiB/366.0 KiB (621.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000068_url.xml to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068_url.xml\nCompleted 144.1 KiB/366.0 KiB (621.0 KiB/s) with 3 file(s) remaining\rCompleted 193.3 KiB/366.0 KiB (818.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000068.png to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.png\nCompleted 193.3 KiB/366.0 KiB (818.5 KiB/s) with 2 file(s) remaining\rCompleted 361.5 KiB/366.0 KiB (1.5 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000068.pdf to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.pdf\nCompleted 361.5 KiB/366.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 366.0 KiB/366.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000068.m to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/contents/BIOMD0000000068.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (140.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d30dcacb55678b4bb3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000068_url.sedml\ncreating dataset /BIOMD0000000068_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-407f07e0-96cd5082-f9d4-e97b65-8a6b84, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000068_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-407f07e0-96cd5082-6fee-835d96-023123, chunk_size: (14, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000068_url.sedml\ncreating attribute uri in /BIOMD0000000068_url.sedml\ncreating attribute _type in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000068_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000068_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000068_url.sedml\ncreate_links: /BIOMD0000000068_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000068_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000068_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000068_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000068_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000068_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000068_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000068_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000068_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107d30dcacb55678b4bb3\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":1.368337,"sedDocuments":[{"location":"BIOMD0000000068_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  BIOMD0000000068_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: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000068_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":0.952157,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.136937,"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":0.156951,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Phser","status":"SUCCEEDED"},{"id":"autogen_task1_Thr","status":"SUCCEEDED"},{"id":"autogen_task1_Cystathionine","status":"SUCCEEDED"},{"id":"autogen_task1_Hser","status":"SUCCEEDED"},{"id":"autogen_task1_Phi","status":"SUCCEEDED"},{"id":"autogen_task1_Cys","status":"SUCCEEDED"},{"id":"autogen_task1_AdoMet","status":"SUCCEEDED"},{"id":"autogen_task1_CGS","status":"SUCCEEDED"},{"id":"autogen_task1_TS","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_vCys","status":"SUCCEEDED"},{"id":"autogen_task1_vThr","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.542961,"curves":[{"id":"autogen_curve_task1_Phser","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Thr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cystathionine","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Hser","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Phi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cys","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AdoMet","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CGS","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TS","status":"SUCCEEDED"}]}]}]}