{"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    441      0 --:--:-- --:--:-- --:--:--   442\n\r100  183k  100  183k    0     0   439k      0 --:--:-- --:--:-- --:--:--  439k\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 (25.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (40.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000127_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000127_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/reports.h5 (deflated 83%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 29.3 KiB/29.3 KiB (440.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/outputs/reports.h5\nCompleted 14.7 KiB/35.1 KiB (196.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/output.zip\nCompleted 14.7 KiB/35.1 KiB (196.5 KiB/s) with 3 file(s) remaining\rCompleted 25.4 KiB/35.1 KiB (230.1 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000127_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/outputs/BIOMD0000000127_url.sedml/autogen_plot_for_task1.pdf\nCompleted 25.4 KiB/35.1 KiB (230.1 KiB/s) with 2 file(s) remaining\rCompleted 32.5 KiB/35.1 KiB (273.9 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/outputs/plots.zip\nCompleted 32.5 KiB/35.1 KiB (273.9 KiB/s) with 1 file(s) remaining\rCompleted 35.1 KiB/35.1 KiB (275.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000127-biopax2.owl  \n  inflating: contents/BIOMD0000000127-biopax3.owl  \n  inflating: contents/BIOMD0000000127-matlab.m  \n  inflating: contents/BIOMD0000000127-octave.m  \n  inflating: contents/BIOMD0000000127.m  \n  inflating: contents/BIOMD0000000127.ode  \n  inflating: contents/BIOMD0000000127.pdf  \n  inflating: contents/BIOMD0000000127.png  \n  inflating: contents/BIOMD0000000127.svg  \n  inflating: contents/BIOMD0000000127_url.sedml  \n  inflating: contents/BIOMD0000000127_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 4.2 KiB/248.0 KiB (53.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000127-biopax2.owl to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127-biopax2.owl\nCompleted 4.2 KiB/248.0 KiB (53.5 KiB/s) with 14 file(s) remaining\rCompleted 9.2 KiB/248.0 KiB (75.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000127.png to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127.png\nCompleted 9.2 KiB/248.0 KiB (75.6 KiB/s) with 13 file(s) remaining\rCompleted 10.6 KiB/248.0 KiB (81.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000127.ode to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127.ode\nCompleted 10.6 KiB/248.0 KiB (81.5 KiB/s) with 12 file(s) remaining\rCompleted 21.1 KiB/248.0 KiB (149.5 KiB/s) with 12 file(s) remaining\rCompleted 148.4 KiB/248.0 KiB (1.0 MiB/s) with 12 file(s) remaining \rupload: contents/BIOMD0000000127_url.xml to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127_url.xml\nCompleted 148.4 KiB/248.0 KiB (1.0 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000127.pdf to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127.pdf\nCompleted 148.4 KiB/248.0 KiB (1.0 MiB/s) with 10 file(s) remaining\rCompleted 149.2 KiB/248.0 KiB (1.0 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000127.svg to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127.svg\nCompleted 149.2 KiB/248.0 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 153.5 KiB/248.0 KiB (1.0 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000127-biopax3.owl to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127-biopax3.owl\nCompleted 153.5 KiB/248.0 KiB (1.0 MiB/s) with 8 file(s) remaining\rCompleted 156.6 KiB/248.0 KiB (1.0 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000127-matlab.m to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127-matlab.m\nCompleted 156.6 KiB/248.0 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 159.7 KiB/248.0 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000127.m to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127.m\nCompleted 159.7 KiB/248.0 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 162.7 KiB/248.0 KiB (1.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000127-octave.m to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127-octave.m\nCompleted 162.7 KiB/248.0 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 169.8 KiB/248.0 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000127_url.sedml to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/BIOMD0000000127_url.sedml\nCompleted 169.8 KiB/248.0 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 170.0 KiB/248.0 KiB (896.5 KiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/curation_notes.txt\nCompleted 170.0 KiB/248.0 KiB (896.5 KiB/s) with 3 file(s) remaining\rCompleted 242.9 KiB/248.0 KiB (1.2 MiB/s) with 3 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/curation_image.png\nCompleted 242.9 KiB/248.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 244.6 KiB/248.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/manifest.xml\nCompleted 244.6 KiB/248.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 248.0 KiB/248.0 KiB (945.9 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (125.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c422321246e8866d9fc0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000127_url.sedml\ncreating dataset /BIOMD0000000127_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-b3bc5e98-8cb5fd86-4ba0-0d2891-45cce2, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000127_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-b3bc5e98-8cb5fd86-6a12-6e73ce-49c891, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000127_url.sedml\ncreating attribute uri in /BIOMD0000000127_url.sedml\ncreating attribute _type in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000127_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000127_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000127_url.sedml\ncreate_links: /BIOMD0000000127_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000127_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000127_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000127_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000127_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000127_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000127_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000127_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000127_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c422321246e8866d9fc0\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 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... 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":1.182268,"sedDocuments":[{"location":"BIOMD0000000127_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  BIOMD0000000127_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: BIOMD0000000127_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":0.830978,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.102885,"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":0.142633,"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":0.481607,"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"}]}]}]}