{"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    517      0 --:--:-- --:--:-- --:--:--   518\n\r100  288k  100  288k    0     0   752k      0 --:--:-- --:--:-- --:--:--  752k\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 (17.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (49.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/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/BIOMD0000000318_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000318_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 231.1 KiB/231.1 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/outputs/reports.h5\nCompleted 13.1 KiB/247.3 KiB (115.9 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000318_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/outputs/BIOMD0000000318_url.sedml/autogen_plot_for_task1.pdf\nCompleted 13.1 KiB/247.3 KiB (115.9 KiB/s) with 3 file(s) remaining\rCompleted 22.9 KiB/247.3 KiB (192.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/outputs/plots.zip\nCompleted 22.9 KiB/247.3 KiB (192.9 KiB/s) with 2 file(s) remaining\rCompleted 25.5 KiB/247.3 KiB (211.3 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/rawLog.txt\nCompleted 25.5 KiB/247.3 KiB (211.3 KiB/s) with 1 file(s) remaining\rCompleted 247.3 KiB/247.3 KiB (1.8 MiB/s) with 1 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000318-biopax2.owl  \n  inflating: contents/BIOMD0000000318-biopax3.owl  \n  inflating: contents/BIOMD0000000318-matlab.m  \n  inflating: contents/BIOMD0000000318-octave.m  \n  inflating: contents/BIOMD0000000318.m  \n  inflating: contents/BIOMD0000000318.ode  \n  inflating: contents/BIOMD0000000318.pdf  \n  inflating: contents/BIOMD0000000318.png  \n  inflating: contents/BIOMD0000000318.svg  \n  inflating: contents/BIOMD0000000318.vcml  \n  inflating: contents/BIOMD0000000318_url.sedml  \n  inflating: contents/BIOMD0000000318_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 22.7 KiB/564.8 KiB (292.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000318-biopax2.owl to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318-biopax2.owl\nCompleted 22.7 KiB/564.8 KiB (292.1 KiB/s) with 15 file(s) remaining\rCompleted 29.8 KiB/564.8 KiB (272.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000318-octave.m to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318-octave.m\nCompleted 29.8 KiB/564.8 KiB (272.8 KiB/s) with 14 file(s) remaining\rCompleted 37.0 KiB/564.8 KiB (321.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000318-matlab.m to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318-matlab.m\nCompleted 37.0 KiB/564.8 KiB (321.7 KiB/s) with 13 file(s) remaining\rCompleted 69.4 KiB/564.8 KiB (464.1 KiB/s) with 13 file(s) remaining\rCompleted 76.6 KiB/564.8 KiB (507.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000318-biopax3.owl to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318-biopax3.owl\nCompleted 76.6 KiB/564.8 KiB (507.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000318.m to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.m\nCompleted 76.6 KiB/564.8 KiB (507.6 KiB/s) with 11 file(s) remaining\rCompleted 169.2 KiB/564.8 KiB (1.1 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000318.png to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.png\nCompleted 169.2 KiB/564.8 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 211.9 KiB/564.8 KiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000318_url.xml to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318_url.xml\nCompleted 211.9 KiB/564.8 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 429.3 KiB/564.8 KiB (2.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000318.pdf to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.pdf\nCompleted 429.3 KiB/564.8 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 433.5 KiB/564.8 KiB (2.5 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000318.ode to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.ode\nCompleted 433.5 KiB/564.8 KiB (2.5 MiB/s) with 7 file(s) remaining\rCompleted 466.5 KiB/564.8 KiB (2.5 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000318.svg to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.svg\nCompleted 466.5 KiB/564.8 KiB (2.5 MiB/s) with 6 file(s) remaining\rCompleted 481.3 KiB/564.8 KiB (2.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000318_url.sedml to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318_url.sedml\nCompleted 481.3 KiB/564.8 KiB (2.6 MiB/s) with 5 file(s) remaining\rCompleted 531.8 KiB/564.8 KiB (2.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000318.vcml to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/BIOMD0000000318.vcml\nCompleted 531.8 KiB/564.8 KiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 558.5 KiB/564.8 KiB (2.5 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/curation_image.png\nCompleted 558.5 KiB/564.8 KiB (2.5 MiB/s) with 3 file(s) remaining\rCompleted 558.7 KiB/564.8 KiB (2.5 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/curation_notes.txt\nCompleted 558.7 KiB/564.8 KiB (2.5 MiB/s) with 2 file(s) remaining\rCompleted 563.0 KiB/564.8 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/metadata.rdf\nCompleted 563.0 KiB/564.8 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 564.8 KiB/564.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (125.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a27f977b666965503b5b9/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000318_url.sedml\ncreating dataset /BIOMD0000000318_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-b44830e7-e6600b36-34d9-138515-82a065, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000318_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-b44830e7-e6600b36-77fb-508e49-5be103, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000318_url.sedml\ncreating attribute uri in /BIOMD0000000318_url.sedml\ncreating attribute _type in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000318_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000318_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000318_url.sedml\ncreate_links: /BIOMD0000000318_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000318_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000318_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000318_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000318_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000318_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000318_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000318_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000318_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a27f977b666965503b5b9\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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 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":1.3747,"sedDocuments":[{"location":"BIOMD0000000318_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  BIOMD0000000318_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000318_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":0.996245,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.183482,"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":0.249644,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_MC","status":"SUCCEEDED"},{"id":"autogen_task1_EF","status":"SUCCEEDED"},{"id":"autogen_task1_CD","status":"SUCCEEDED"},{"id":"autogen_task1_CE","status":"SUCCEEDED"},{"id":"autogen_task1_RB","status":"SUCCEEDED"},{"id":"autogen_task1_RE","status":"SUCCEEDED"},{"id":"autogen_task1_RP","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_r4","status":"SUCCEEDED"},{"id":"autogen_task1_r5","status":"SUCCEEDED"},{"id":"autogen_task1_r6","status":"SUCCEEDED"},{"id":"autogen_task1_r7","status":"SUCCEEDED"},{"id":"autogen_task1_r8","status":"SUCCEEDED"},{"id":"autogen_task1_r9","status":"SUCCEEDED"},{"id":"autogen_task1_r10","status":"SUCCEEDED"},{"id":"autogen_task1_r11","status":"SUCCEEDED"},{"id":"autogen_task1_r12","status":"SUCCEEDED"},{"id":"autogen_task1_r13","status":"SUCCEEDED"},{"id":"autogen_task1_r14","status":"SUCCEEDED"},{"id":"autogen_task1_r15","status":"SUCCEEDED"},{"id":"autogen_task1_r16","status":"SUCCEEDED"},{"id":"autogen_task1_r17","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.431644,"curves":[{"id":"autogen_curve_task1_MC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CE","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RB","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RE","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RP","status":"SUCCEEDED"}]}]}]}