{"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    468      0 --:--:-- --:--:-- --:--:--   469\n\r100  166k  100  166k    0     0   395k      0 --:--:-- --:--:-- --:--:--  395k\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 (17.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (33.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/BIOMD0000000368_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000368_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 126.2 KiB/126.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/outputs/reports.h5\nCompleted 112.2 KiB/128.1 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/output.zip\nCompleted 112.2 KiB/128.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 117.5 KiB/128.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/outputs/plots.zip\nCompleted 117.5 KiB/128.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 120.1 KiB/128.1 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/rawLog.txt\nCompleted 120.1 KiB/128.1 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 128.1 KiB/128.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000368_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/outputs/BIOMD0000000368_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000368-biopax2.owl  \n  inflating: contents/BIOMD0000000368-biopax3.owl  \n  inflating: contents/BIOMD0000000368-matlab.m  \n  inflating: contents/BIOMD0000000368-octave.m  \n  inflating: contents/BIOMD0000000368.m  \n  inflating: contents/BIOMD0000000368.ode  \n  inflating: contents/BIOMD0000000368.pdf  \n  inflating: contents/BIOMD0000000368.png  \n  inflating: contents/BIOMD0000000368.sci  \n  inflating: contents/BIOMD0000000368.svg  \n  inflating: contents/BIOMD0000000368_url.sedml  \n  inflating: contents/BIOMD0000000368_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 3.7 KiB/244.1 KiB (57.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000368-biopax2.owl to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368-biopax2.owl\nCompleted 3.7 KiB/244.1 KiB (57.0 KiB/s) with 15 file(s) remaining\rCompleted 8.7 KiB/244.1 KiB (76.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000368.png to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.png\nCompleted 8.7 KiB/244.1 KiB (76.3 KiB/s) with 14 file(s) remaining\rCompleted 13.2 KiB/244.1 KiB (111.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000368-matlab.m to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368-matlab.m\nCompleted 13.2 KiB/244.1 KiB (111.3 KiB/s) with 13 file(s) remaining\rCompleted 13.3 KiB/244.1 KiB (100.4 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/curation_notes.txt\nCompleted 13.3 KiB/244.1 KiB (100.4 KiB/s) with 12 file(s) remaining\rCompleted 17.9 KiB/244.1 KiB (128.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000368-octave.m to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368-octave.m\nCompleted 17.9 KiB/244.1 KiB (128.2 KiB/s) with 11 file(s) remaining\rCompleted 19.9 KiB/244.1 KiB (140.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000368.sci to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.sci\nCompleted 19.9 KiB/244.1 KiB (140.5 KiB/s) with 10 file(s) remaining\rCompleted 31.7 KiB/244.1 KiB (216.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000368_url.sedml to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368_url.sedml\nCompleted 31.7 KiB/244.1 KiB (216.1 KiB/s) with 9 file(s) remaining\rCompleted 41.9 KiB/244.1 KiB (274.3 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000368_url.xml to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368_url.xml\nCompleted 41.9 KiB/244.1 KiB (274.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000368.svg to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.svg\nCompleted 41.9 KiB/244.1 KiB (274.3 KiB/s) with 7 file(s) remaining\rCompleted 94.1 KiB/244.1 KiB (547.7 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/curation_image.png\nCompleted 94.1 KiB/244.1 KiB (547.7 KiB/s) with 6 file(s) remaining\rCompleted 96.3 KiB/244.1 KiB (543.2 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/metadata.rdf\nCompleted 96.3 KiB/244.1 KiB (543.2 KiB/s) with 5 file(s) remaining\rCompleted 98.2 KiB/244.1 KiB (543.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/manifest.xml\nCompleted 98.2 KiB/244.1 KiB (543.9 KiB/s) with 4 file(s) remaining\rCompleted 100.3 KiB/244.1 KiB (501.2 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000368.ode to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.ode\nCompleted 100.3 KiB/244.1 KiB (501.2 KiB/s) with 3 file(s) remaining\rCompleted 235.1 KiB/244.1 KiB (1.1 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000368.pdf to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.pdf\nCompleted 235.1 KiB/244.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 239.6 KiB/244.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000368.m to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368.m\nCompleted 239.6 KiB/244.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 244.1 KiB/244.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000368-biopax3.owl to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/contents/BIOMD0000000368-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (124.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bbe49c0d898ffde18bf/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-05-26 16:00:04,355 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-d65326ce-0881279c-f9c0-312038-c2d9e1/value?select=%5B0%3A20%2C0%3A1001%5D&domain=%2Fresults%2F64710bbe49c0d898ffde18bf (Caused by ResponseError('too many 500 error responses',))\ncreating group /BIOMD0000000368_url.sedml\ncreating dataset /BIOMD0000000368_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-d65326ce-0881279c-9780-e7e36e-e5920a, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000368_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-d65326ce-0881279c-f9c0-312038-c2d9e1, chunk_size: (20, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000368_url.sedml\ncreating attribute uri in /BIOMD0000000368_url.sedml\ncreating attribute _type in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000368_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000368_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000368_url.sedml\ncreate_links: /BIOMD0000000368_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000368_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000368_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000368_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000368_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000368_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000368_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000368_url.sedml/autogen_report_for_task1\nERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-d65326ce-0881279c-f9c0-312038-c2d9e1/value?select=%5B0%3A20%2C0%3A1001%5D&domain=%2Fresults%2F64710bbe49c0d898ffde18bf (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /BIOMD0000000368_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710bbe49c0d898ffde18bf\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 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 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":13.38244,"sedDocuments":[{"location":"BIOMD0000000368_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  BIOMD0000000368_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000368_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":13.08693,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":12.511529,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.175571,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_task1_Z3","status":"SUCCEEDED"},{"id":"autogen_task1_Z4","status":"SUCCEEDED"},{"id":"autogen_task1_E1","status":"SUCCEEDED"},{"id":"autogen_task1_E2","status":"SUCCEEDED"},{"id":"autogen_task1_E3","status":"SUCCEEDED"},{"id":"autogen_task1_E4","status":"SUCCEEDED"},{"id":"autogen_task1_mu1","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_mu23","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_mu4","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_mu5","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.289016,"curves":[{"id":"autogen_curve_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E4","status":"SUCCEEDED"}]}]}]}