{"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    422      0 --:--:-- --:--:-- --:--:--   422\r100   139  100   139    0     0    416      0 --:--:-- --:--:-- --:--:--   416\n\r100 68350  100 68350    0     0   150k      0 --:--:-- --:--:-- --:--:--  150k\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 (19.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (38.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/Ferrel2011_V3.sedml/ (stored 0%)\n  adding: outputs/Ferrel2011_V3.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 65%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.2 KiB/31.2 KiB (323.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/outputs/reports.h5\nCompleted 22.8 KiB/47.4 KiB (189.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/output.zip\nCompleted 22.8 KiB/47.4 KiB (189.7 KiB/s) with 3 file(s) remaining\rCompleted 35.8 KiB/47.4 KiB (275.3 KiB/s) with 3 file(s) remaining\rupload: outputs/Ferrel2011_V3.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/outputs/Ferrel2011_V3.sedml/plot_1_task1.pdf\nCompleted 35.8 KiB/47.4 KiB (275.3 KiB/s) with 2 file(s) remaining\rCompleted 38.4 KiB/47.4 KiB (266.0 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/rawLog.txt\nCompleted 38.4 KiB/47.4 KiB (266.0 KiB/s) with 1 file(s) remaining\rCompleted 47.4 KiB/47.4 KiB (322.0 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Ferrel2011_V3-biopax2.owl  \n  inflating: contents/Ferrel2011_V3-biopax3.owl  \n  inflating: contents/Ferrel2011_V3-matlab.m  \n  inflating: contents/Ferrel2011_V3-octave.m  \n  inflating: contents/Ferrel2011_V3.cps  \n  inflating: contents/Ferrel2011_V3.ode  \n  inflating: contents/Ferrel2011_V3.sedml  \n  inflating: contents/Ferrel2011_V3.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 10.1 KiB/205.2 KiB (75.1 KiB/s) with 12 file(s) remaining\rupload: contents/Ferrel2011_V3-biopax2.owl to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3-biopax2.owl\nCompleted 10.1 KiB/205.2 KiB (75.1 KiB/s) with 11 file(s) remaining\rCompleted 11.4 KiB/205.2 KiB (71.1 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/manifest.xml\nCompleted 11.4 KiB/205.2 KiB (71.1 KiB/s) with 10 file(s) remaining\rCompleted 16.1 KiB/205.2 KiB (95.4 KiB/s) with 10 file(s) remaining\rupload: contents/Ferrel2011_V3-octave.m to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3-octave.m\nCompleted 16.1 KiB/205.2 KiB (95.4 KiB/s) with 9 file(s) remaining\rCompleted 20.8 KiB/205.2 KiB (120.6 KiB/s) with 9 file(s) remaining\rupload: contents/Ferrel2011_V3-matlab.m to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3-matlab.m\nCompleted 20.8 KiB/205.2 KiB (120.6 KiB/s) with 8 file(s) remaining\rCompleted 23.9 KiB/205.2 KiB (135.9 KiB/s) with 8 file(s) remaining\rupload: contents/Ferrel2011_V3.ode to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3.ode\nCompleted 23.9 KiB/205.2 KiB (135.9 KiB/s) with 7 file(s) remaining\rCompleted 26.4 KiB/205.2 KiB (146.1 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/metadata.rdf\nCompleted 26.4 KiB/205.2 KiB (146.1 KiB/s) with 6 file(s) remaining\rCompleted 61.8 KiB/205.2 KiB (338.8 KiB/s) with 6 file(s) remaining\rupload: contents/Ferrel2011_V3.xml to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3.xml\nCompleted 61.8 KiB/205.2 KiB (338.8 KiB/s) with 5 file(s) remaining\rCompleted 61.9 KiB/205.2 KiB (336.4 KiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/curation_notes.txt\nCompleted 61.9 KiB/205.2 KiB (336.4 KiB/s) with 4 file(s) remaining\rCompleted 132.0 KiB/205.2 KiB (620.7 KiB/s) with 4 file(s) remaining\rupload: contents/Ferrel2011_V3.cps to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3.cps\nCompleted 132.0 KiB/205.2 KiB (620.7 KiB/s) with 3 file(s) remaining\rCompleted 177.2 KiB/205.2 KiB (787.1 KiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/curation_image.png\nCompleted 177.2 KiB/205.2 KiB (787.1 KiB/s) with 2 file(s) remaining\rCompleted 191.6 KiB/205.2 KiB (819.5 KiB/s) with 2 file(s) remaining\rupload: contents/Ferrel2011_V3.sedml to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3.sedml\nCompleted 191.6 KiB/205.2 KiB (819.5 KiB/s) with 1 file(s) remaining\rCompleted 205.2 KiB/205.2 KiB (731.2 KiB/s) with 1 file(s) remaining\rupload: contents/Ferrel2011_V3-biopax3.owl to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/contents/Ferrel2011_V3-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (79.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caa0fb37cdb9ae75592/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:29:30,849 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-d1a18fd9-2ea028c6-56ff-04c786-55d1fe/value?select=%5B0%3A23%2C0%3A101%5D&domain=%2Fresults%2F647a5caa0fb37cdb9ae75592 (Caused by ResponseError('too many 500 error responses',))\ncreating group /Ferrel2011_V3.sedml\ncreating dataset /Ferrel2011_V3.sedml/autogen_report_for_task1, shape: (23, 101), type: float64\ndataset created, uuid: d-d1a18fd9-2ea028c6-56ff-04c786-55d1fe, chunk_size: (23, 101)\ncreating dataset /Ferrel2011_V3.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-d1a18fd9-2ea028c6-8c3c-8f3575-2a5755, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Ferrel2011_V3.sedml\ncreating attribute uri in /Ferrel2011_V3.sedml\ncreating attribute _type in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute uri in /Ferrel2011_V3.sedml/autogen_report_for_task1\ncreating attribute _type in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlId in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute sedmlName in /Ferrel2011_V3.sedml/plot_1_task1\ncreating attribute uri in /Ferrel2011_V3.sedml/plot_1_task1\ncreate_links: /\ngot link: Ferrel2011_V3.sedml\ncreate_links: /Ferrel2011_V3.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Ferrel2011_V3.sedml/autogen_report_for_task1 to tgt: /Ferrel2011_V3.sedml/autogen_report_for_task1, shape: (23, 101), type: float64\niterating over chunks for /Ferrel2011_V3.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-d1a18fd9-2ea028c6-56ff-04c786-55d1fe/value?select=%5B0%3A23%2C0%3A101%5D&domain=%2Fresults%2F647a5caa0fb37cdb9ae75592 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Ferrel2011_V3.sedml/autogen_report_for_task1\nwrite_dataset src: /Ferrel2011_V3.sedml/plot_1_task1 to tgt: /Ferrel2011_V3.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Ferrel2011_V3.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Ferrel2011_V3.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5caa0fb37cdb9ae75592\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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.407434,"sedDocuments":[{"location":"Ferrel2011_V3.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  Ferrel2011_V3.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Ferrel2011_V3.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":0.801262,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.2185,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.369694,"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":0.070984,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_APC_active","status":"SUCCEEDED"},{"id":"autogen_task1_CDK1_active","status":"SUCCEEDED"},{"id":"autogen_task1_Plk1_active","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_a3","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_b3","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_n1","status":"SUCCEEDED"},{"id":"autogen_task1_n2","status":"SUCCEEDED"},{"id":"autogen_task1_n3","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1_Cdk1_activation_by_cyclin_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_R2_Cdk1_inactivation_by_APC_active","status":"SUCCEEDED"},{"id":"autogen_task1_R3_APC_activation_by_Cdk1_active","status":"SUCCEEDED"},{"id":"autogen_task1_R4_APC_Inactivation","status":"SUCCEEDED"},{"id":"autogen_task1_R5_Plk1_activation_by","status":"SUCCEEDED"},{"id":"autogen_task1_R6_Plk1_inactivation","status":"SUCCEEDED"}]}]}]}