{"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    435      0 --:--:-- --:--:-- --:--:--   435\n\r100  164k  100  164k    0     0   344k      0 --:--:-- --:--:-- --:--:--  344k\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 (26.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/rawLog.txt\nCompleted 2.7 KiB/2.7 KiB (37.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000421_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000421_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 30%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 71.7 KiB/71.7 KiB (789.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/outputs/reports.h5\nCompleted 58.7 KiB/77.2 KiB (766.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/output.zip\nCompleted 58.7 KiB/77.2 KiB (766.9 KiB/s) with 3 file(s) remaining\rCompleted 65.0 KiB/77.2 KiB (619.0 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/outputs/plots.zip\nCompleted 65.0 KiB/77.2 KiB (619.0 KiB/s) with 2 file(s) remaining\rCompleted 74.6 KiB/77.2 KiB (691.8 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000421_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/outputs/BIOMD0000000421_url.sedml/autogen_plot_for_task1.pdf\nCompleted 74.6 KiB/77.2 KiB (691.8 KiB/s) with 1 file(s) remaining\rCompleted 77.2 KiB/77.2 KiB (668.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000421-biopax2.owl  \n  inflating: contents/BIOMD0000000421-biopax3.owl  \n  inflating: contents/BIOMD0000000421-matlab.m  \n  inflating: contents/BIOMD0000000421-octave.m  \n  inflating: contents/BIOMD0000000421.m  \n  inflating: contents/BIOMD0000000421.ode  \n  inflating: contents/BIOMD0000000421.pdf  \n  inflating: contents/BIOMD0000000421.png  \n  inflating: contents/BIOMD0000000421.sci  \n  inflating: contents/BIOMD0000000421.svg  \n  inflating: contents/BIOMD0000000421.vcml  \n  inflating: contents/BIOMD0000000421_url.sedml  \n  inflating: contents/BIOMD0000000421_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 8.0 KiB/269.1 KiB (88.5 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000421-biopax3.owl to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421-biopax3.owl\nCompleted 8.0 KiB/269.1 KiB (88.5 KiB/s) with 16 file(s) remaining\rCompleted 12.1 KiB/269.1 KiB (103.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000421-matlab.m to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421-matlab.m\nCompleted 12.1 KiB/269.1 KiB (103.7 KiB/s) with 15 file(s) remaining\rCompleted 21.2 KiB/269.1 KiB (173.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000421.png to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.png\nCompleted 21.2 KiB/269.1 KiB (173.5 KiB/s) with 14 file(s) remaining\rCompleted 27.3 KiB/269.1 KiB (211.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000421-biopax2.owl to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421-biopax2.owl\nCompleted 27.3 KiB/269.1 KiB (211.4 KiB/s) with 13 file(s) remaining\rCompleted 31.7 KiB/269.1 KiB (226.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000421.sci to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.sci\nCompleted 31.7 KiB/269.1 KiB (226.4 KiB/s) with 12 file(s) remaining\rCompleted 48.9 KiB/269.1 KiB (345.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000421.vcml to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.vcml\nCompleted 48.9 KiB/269.1 KiB (345.8 KiB/s) with 11 file(s) remaining\rCompleted 54.9 KiB/269.1 KiB (375.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000421.svg to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.svg\nCompleted 54.9 KiB/269.1 KiB (375.4 KiB/s) with 10 file(s) remaining\rCompleted 55.1 KiB/269.1 KiB (363.5 KiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/curation_notes.txt\nCompleted 55.1 KiB/269.1 KiB (363.5 KiB/s) with 9 file(s) remaining\rCompleted 65.6 KiB/269.1 KiB (412.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000421_url.sedml to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421_url.sedml\nCompleted 65.6 KiB/269.1 KiB (412.5 KiB/s) with 8 file(s) remaining\rCompleted 67.6 KiB/269.1 KiB (403.8 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/manifest.xml\nCompleted 67.6 KiB/269.1 KiB (403.8 KiB/s) with 7 file(s) remaining\rCompleted 71.7 KiB/269.1 KiB (415.3 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/metadata.rdf\nCompleted 71.7 KiB/269.1 KiB (415.3 KiB/s) with 6 file(s) remaining\rCompleted 89.8 KiB/269.1 KiB (496.2 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/curation_image.png\nCompleted 89.8 KiB/269.1 KiB (496.2 KiB/s) with 5 file(s) remaining\rCompleted 104.6 KiB/269.1 KiB (556.9 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000421_url.xml to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421_url.xml\nCompleted 104.6 KiB/269.1 KiB (556.9 KiB/s) with 4 file(s) remaining\rCompleted 108.7 KiB/269.1 KiB (556.6 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000421-octave.m to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421-octave.m\nCompleted 108.7 KiB/269.1 KiB (556.6 KiB/s) with 3 file(s) remaining\rCompleted 110.8 KiB/269.1 KiB (551.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000421.ode to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.ode\nCompleted 110.8 KiB/269.1 KiB (551.5 KiB/s) with 2 file(s) remaining\rCompleted 265.0 KiB/269.1 KiB (1.2 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000421.pdf to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.pdf\nCompleted 265.0 KiB/269.1 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 269.1 KiB/269.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000421.m to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/contents/BIOMD0000000421.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (105.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c6d0dcacb55678bd6a5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-05-26 16:00:26,540 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-699c3eaa-1fc0f6bd-cf45-ec5b11-688470/value?select=%5B0%3A3%2C0%3A1001%5D&domain=%2Fresults%2F64710c6d0dcacb55678bd6a5 (Caused by ResponseError('too many 500 error responses',))\ncreating group /BIOMD0000000421_url.sedml\ncreating dataset /BIOMD0000000421_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-699c3eaa-1fc0f6bd-cf45-ec5b11-688470, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000421_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-699c3eaa-1fc0f6bd-77da-9a76d1-f0f2e4, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000421_url.sedml\ncreating attribute uri in /BIOMD0000000421_url.sedml\ncreating attribute _type in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000421_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000421_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000421_url.sedml\ncreate_links: /BIOMD0000000421_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000421_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000421_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000421_url.sedml/autogen_plot_for_task1\nERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-699c3eaa-1fc0f6bd-cf45-ec5b11-688470/value?select=%5B0%3A3%2C0%3A1001%5D&domain=%2Fresults%2F64710c6d0dcacb55678bd6a5 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /BIOMD0000000421_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000421_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000421_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000421_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000421_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c6d0dcacb55678bd6a5\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.122397,"sedDocuments":[{"location":"BIOMD0000000421_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  BIOMD0000000421_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000421_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":0.763549,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.114615,"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":0.178479,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_P1","status":"SUCCEEDED"},{"id":"autogen_task1_Target","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_Ksp","status":"SUCCEEDED"},{"id":"autogen_task1_P2","status":"SUCCEEDED"},{"id":"autogen_task1_dsp1ksp","status":"SUCCEEDED"},{"id":"autogen_task1_dsp1p2kd","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_ku","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_univ","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.333709,"curves":[{"id":"autogen_curve_task1_P1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Target","status":"SUCCEEDED"}]}]}]}