{"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    443      0 --:--:-- --:--:-- --:--:--   442\n\r100  135k  100  135k    0     0   324k      0 --:--:-- --:--:-- --:--:--  324k\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 (25.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (35.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/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/BIOMD0000000133_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000133_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 45%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 53.1 KiB/53.1 KiB (594.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/outputs/reports.h5\nCompleted 10.8 KiB/59.4 KiB (161.7 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000133_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/outputs/BIOMD0000000133_url.sedml/autogen_plot_for_task1.pdf\nCompleted 10.8 KiB/59.4 KiB (161.7 KiB/s) with 3 file(s) remaining\rCompleted 18.0 KiB/59.4 KiB (164.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/outputs/plots.zip\nCompleted 18.0 KiB/59.4 KiB (164.5 KiB/s) with 2 file(s) remaining\rCompleted 56.7 KiB/59.4 KiB (473.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/output.zip\nCompleted 56.7 KiB/59.4 KiB (473.5 KiB/s) with 1 file(s) remaining\rCompleted 59.4 KiB/59.4 KiB (427.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000133-biopax2.owl  \n  inflating: contents/BIOMD0000000133-biopax3.owl  \n  inflating: contents/BIOMD0000000133-matlab.m  \n  inflating: contents/BIOMD0000000133-octave.m  \n  inflating: contents/BIOMD0000000133.m  \n  inflating: contents/BIOMD0000000133.pdf  \n  inflating: contents/BIOMD0000000133.png  \n  inflating: contents/BIOMD0000000133.svg  \n  inflating: contents/BIOMD0000000133_url.sedml  \n  inflating: contents/BIOMD0000000133_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/197.2 KiB (56.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000133-octave.m to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133-octave.m\nCompleted 3.5 KiB/197.2 KiB (56.8 KiB/s) with 13 file(s) remaining\rCompleted 7.0 KiB/197.2 KiB (61.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000133.m to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133.m\nCompleted 7.0 KiB/197.2 KiB (61.5 KiB/s) with 12 file(s) remaining\rCompleted 20.2 KiB/197.2 KiB (160.8 KiB/s) with 12 file(s) remaining\rCompleted 34.6 KiB/197.2 KiB (273.2 KiB/s) with 12 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/curation_image.png\nCompleted 34.6 KiB/197.2 KiB (273.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000133_url.xml to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133_url.xml\nCompleted 34.6 KiB/197.2 KiB (273.2 KiB/s) with 10 file(s) remaining\rCompleted 35.4 KiB/197.2 KiB (276.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000133.svg to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133.svg\nCompleted 35.4 KiB/197.2 KiB (276.5 KiB/s) with 9 file(s) remaining\rCompleted 40.5 KiB/197.2 KiB (303.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000133.png to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133.png\nCompleted 40.5 KiB/197.2 KiB (303.6 KiB/s) with 8 file(s) remaining\rCompleted 44.2 KiB/197.2 KiB (321.5 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000133-biopax3.owl to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133-biopax3.owl\nCompleted 44.2 KiB/197.2 KiB (321.5 KiB/s) with 7 file(s) remaining\rCompleted 45.8 KiB/197.2 KiB (330.6 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/manifest.xml\nCompleted 45.8 KiB/197.2 KiB (330.6 KiB/s) with 6 file(s) remaining\rCompleted 179.1 KiB/197.2 KiB (1.2 MiB/s) with 6 file(s) remaining \rupload: contents/BIOMD0000000133.pdf to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133.pdf\nCompleted 179.1 KiB/197.2 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 182.6 KiB/197.2 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000133-matlab.m to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133-matlab.m\nCompleted 182.6 KiB/197.2 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 186.2 KiB/197.2 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000133-biopax2.owl to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133-biopax2.owl\nCompleted 186.2 KiB/197.2 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 186.3 KiB/197.2 KiB (985.5 KiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/curation_notes.txt\nCompleted 186.3 KiB/197.2 KiB (985.5 KiB/s) with 2 file(s) remaining\rCompleted 190.1 KiB/197.2 KiB (978.4 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/metadata.rdf\nCompleted 190.1 KiB/197.2 KiB (978.4 KiB/s) with 1 file(s) remaining\rCompleted 197.2 KiB/197.2 KiB (1004.5 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000133_url.sedml to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/contents/BIOMD0000000133_url.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (123.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c42d321246e8866da0ea/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000133_url.sedml\ncreating dataset /BIOMD0000000133_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-09203738-9e327c04-5630-7c2014-efb2eb, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000133_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-09203738-9e327c04-db8a-3e8b43-0d1633, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000133_url.sedml\ncreating attribute uri in /BIOMD0000000133_url.sedml\ncreating attribute _type in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000133_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000133_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000133_url.sedml\ncreate_links: /BIOMD0000000133_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000133_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000133_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000133_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000133_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000133_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000133_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000133_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000133_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c42d321246e8866da0ea\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":1.188055,"sedDocuments":[{"location":"BIOMD0000000133_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  BIOMD0000000133_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 10 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000133_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":0.81484,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.107686,"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":0.129101,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_task1_i","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.479478,"curves":[{"id":"autogen_curve_task1_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_b","status":"SUCCEEDED"},{"id":"autogen_curve_task1_c","status":"SUCCEEDED"},{"id":"autogen_curve_task1_d","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i","status":"SUCCEEDED"},{"id":"autogen_curve_task1_v","status":"SUCCEEDED"},{"id":"autogen_curve_task1_u","status":"SUCCEEDED"}]}]}]}