{"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    446      0 --:--:-- --:--:-- --:--:--   446\n\r100  252k  100  252k    0     0   556k      0 --:--:-- --:--:-- --:--:--  556k\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 (14.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (36.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/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/Dubey2007_model2.sedml/ (stored 0%)\n  adding: outputs/Dubey2007_model2.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 62%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 41.2 KiB/41.2 KiB (382.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/outputs/reports.h5\nCompleted 25.8 KiB/46.4 KiB (227.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/output.zip\nCompleted 25.8 KiB/46.4 KiB (227.3 KiB/s) with 3 file(s) remaining\rCompleted 33.2 KiB/46.4 KiB (226.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/outputs/plots.zip\nCompleted 33.2 KiB/46.4 KiB (226.7 KiB/s) with 2 file(s) remaining\rCompleted 43.8 KiB/46.4 KiB (287.8 KiB/s) with 2 file(s) remaining\rupload: outputs/Dubey2007_model2.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/outputs/Dubey2007_model2.sedml/plot_1_task1.pdf\nCompleted 43.8 KiB/46.4 KiB (287.8 KiB/s) with 1 file(s) remaining\rCompleted 46.4 KiB/46.4 KiB (165.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Dubey2007_model2-biopax2.owl  \n  inflating: contents/Dubey2007_model2-biopax3.owl  \n  inflating: contents/Dubey2007_model2-matlab.m  \n  inflating: contents/Dubey2007_model2-octave.m  \n  inflating: contents/Dubey2007_model2.cps  \n  inflating: contents/Dubey2007_model2.ode  \n  inflating: contents/Dubey2007_model2.sedml  \n  inflating: contents/Dubey2007_model2.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 20.4 KiB/506.7 KiB (184.3 KiB/s) with 12 file(s) remaining\rupload: contents/Dubey2007_model2-biopax3.owl to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2-biopax3.owl\nCompleted 20.4 KiB/506.7 KiB (184.3 KiB/s) with 11 file(s) remaining\rCompleted 276.4 KiB/506.7 KiB (2.3 MiB/s) with 11 file(s) remaining \rCompleted 277.8 KiB/506.7 KiB (1.8 MiB/s) with 11 file(s) remaining \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/manifest.xml\nCompleted 277.8 KiB/506.7 KiB (1.8 MiB/s) with 10 file(s) remaining\rCompleted 278.0 KiB/506.7 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/curation_notes.txt\nCompleted 278.0 KiB/506.7 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 286.7 KiB/506.7 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/Dubey2007_model2-octave.m to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2-octave.m\nCompleted 286.7 KiB/506.7 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 293.0 KiB/506.7 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/Dubey2007_model2.ode to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2.ode\nCompleted 293.0 KiB/506.7 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 295.3 KiB/506.7 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/metadata.rdf\nCompleted 295.3 KiB/506.7 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 309.0 KiB/506.7 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/Dubey2007_model2-biopax2.owl to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2-biopax2.owl\nCompleted 309.0 KiB/506.7 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 317.7 KiB/506.7 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/Dubey2007_model2-matlab.m to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2-matlab.m\nCompleted 317.7 KiB/506.7 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 399.8 KiB/506.7 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/Dubey2007_model2.cps to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2.cps\nCompleted 399.8 KiB/506.7 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 446.1 KiB/506.7 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/Dubey2007_model2.xml to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2.xml\nCompleted 446.1 KiB/506.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 467.0 KiB/506.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/Dubey2007_model2.sedml to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/Dubey2007_model2.sedml\nCompleted 467.0 KiB/506.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 506.7 KiB/506.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (73.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca20fb37cdb9ae75574/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:29:38,313 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-d498e98e-5fd51e99-1822-34ef22-384a7c/value?select=%5B0%3A4%2C0%3A101%5D&domain=%2Fresults%2F647a5ca20fb37cdb9ae75574 (Caused by ResponseError('too many 500 error responses',))\ncreating group /Dubey2007_model2.sedml\ncreating dataset /Dubey2007_model2.sedml/autogen_report_for_task1, shape: (32, 101), type: float64\ndataset created, uuid: d-d498e98e-5fd51e99-91d5-793bba-84288b, chunk_size: (32, 101)\ncreating dataset /Dubey2007_model2.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-d498e98e-5fd51e99-1822-34ef22-384a7c, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Dubey2007_model2.sedml\ncreating attribute uri in /Dubey2007_model2.sedml\ncreating attribute _type in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute uri in /Dubey2007_model2.sedml/autogen_report_for_task1\ncreating attribute _type in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlId in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute sedmlName in /Dubey2007_model2.sedml/plot_1_task1\ncreating attribute uri in /Dubey2007_model2.sedml/plot_1_task1\ncreate_links: /\ngot link: Dubey2007_model2.sedml\ncreate_links: /Dubey2007_model2.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Dubey2007_model2.sedml/autogen_report_for_task1 to tgt: /Dubey2007_model2.sedml/autogen_report_for_task1, shape: (32, 101), type: float64\niterating over chunks for /Dubey2007_model2.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 32, 1), slice(0, 101, 1))\ndone with dataload for /Dubey2007_model2.sedml/autogen_report_for_task1\nwrite_dataset src: /Dubey2007_model2.sedml/plot_1_task1 to tgt: /Dubey2007_model2.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Dubey2007_model2.sedml/plot_1_task1\nERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-d498e98e-5fd51e99-1822-34ef22-384a7c/value?select=%5B0%3A4%2C0%3A101%5D&domain=%2Fresults%2F647a5ca20fb37cdb9ae75574 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Dubey2007_model2.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5ca20fb37cdb9ae75574\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":17.995093,"sedDocuments":[{"location":"Dubey2007_model2.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  Dubey2007_model2.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 32 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Dubey2007_model2.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":17.650424,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.133628,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.302989,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.079799,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_beta0","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_alpha0","status":"SUCCEEDED"},{"id":"autogen_task1_Q0","status":"SUCCEEDED"},{"id":"autogen_task1_delta_0","status":"SUCCEEDED"},{"id":"autogen_task1_theta_0","status":"SUCCEEDED"},{"id":"autogen_task1_delta_1","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_n1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_increase_in_the_amount_of_pathogenic_micro_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_amount_of_pathogenic_micro_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_of_appropriate_immune_response_with_respect_to_pathogen","status":"SUCCEEDED"},{"id":"autogen_task1_Reduction_of_immune_response","status":"SUCCEEDED"},{"id":"autogen_task1_betterment_of_relative_characteristics_of_the_damaged_part_of_the_organ","status":"SUCCEEDED"},{"id":"autogen_task1_removal_of_relative_characteristics_of_the_damaged_part_of_the_organ","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_in_the_concentration_of_toxicant_in_the_environment","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_concentration_of_toxicant_in_the_environment","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_in_the_uptake_concentration_of_toxicant_by_the_body","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_uptake_concentration_of_toxcant_by_the_body","status":"SUCCEEDED"}]}]}]}