{"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    437      0 --:--:-- --:--:-- --:--:--   438\n\r100 44050  100 44050    0     0    99k      0 --:--:-- --:--:-- --:--:--   99k\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/647a5f4f195afd5df176211a/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (30.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/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/Bose2011.sedml/ (stored 0%)\n  adding: outputs/Bose2011.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 64%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.3 KiB/31.3 KiB (268.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/outputs/reports.h5\nCompleted 21.1 KiB/41.1 KiB (176.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/output.zip\nCompleted 21.1 KiB/41.1 KiB (176.5 KiB/s) with 3 file(s) remaining\rCompleted 31.3 KiB/41.1 KiB (210.7 KiB/s) with 3 file(s) remaining\rupload: outputs/Bose2011.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/outputs/Bose2011.sedml/plot_1_task1.pdf\nCompleted 31.3 KiB/41.1 KiB (210.7 KiB/s) with 2 file(s) remaining\rCompleted 38.5 KiB/41.1 KiB (248.6 KiB/s) with 2 file(s) remaining\rCompleted 41.1 KiB/41.1 KiB (261.4 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/rawLog.txt\nCompleted 41.1 KiB/41.1 KiB (261.4 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Bose2011-biopax2.owl  \n  inflating: contents/Bose2011-biopax3.owl  \n  inflating: contents/Bose2011-matlab.m  \n  inflating: contents/Bose2011-octave.m  \n  inflating: contents/Bose2011.cps   \n  inflating: contents/Bose2011.ode   \n  inflating: contents/Bose2011.sedml  \n  inflating: contents/Bose2011.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 9.9 KiB/172.3 KiB (136.2 KiB/s) with 12 file(s) remaining\rupload: contents/Bose2011-biopax2.owl to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011-biopax2.owl\nCompleted 9.9 KiB/172.3 KiB (136.2 KiB/s) with 11 file(s) remaining\rCompleted 15.6 KiB/172.3 KiB (101.9 KiB/s) with 11 file(s) remaining\rupload: contents/Bose2011-octave.m to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011-octave.m\nCompleted 15.6 KiB/172.3 KiB (101.9 KiB/s) with 10 file(s) remaining\rCompleted 21.2 KiB/172.3 KiB (132.8 KiB/s) with 10 file(s) remaining\rupload: contents/Bose2011-matlab.m to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011-matlab.m\nCompleted 21.2 KiB/172.3 KiB (132.8 KiB/s) with 9 file(s) remaining\rCompleted 43.1 KiB/172.3 KiB (251.5 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/curation_image.png\nCompleted 43.1 KiB/172.3 KiB (251.5 KiB/s) with 8 file(s) remaining\rCompleted 55.3 KiB/172.3 KiB (314.3 KiB/s) with 8 file(s) remaining\rupload: contents/Bose2011.sedml to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011.sedml\nCompleted 55.3 KiB/172.3 KiB (314.3 KiB/s) with 7 file(s) remaining\rCompleted 55.6 KiB/172.3 KiB (312.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/curation_notes.txt\nCompleted 55.6 KiB/172.3 KiB (312.2 KiB/s) with 6 file(s) remaining\rCompleted 90.6 KiB/172.3 KiB (500.1 KiB/s) with 6 file(s) remaining\rupload: contents/Bose2011.xml to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011.xml\nCompleted 90.6 KiB/172.3 KiB (500.1 KiB/s) with 5 file(s) remaining\rCompleted 91.9 KiB/172.3 KiB (496.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/manifest.xml\nCompleted 91.9 KiB/172.3 KiB (496.9 KiB/s) with 4 file(s) remaining\rCompleted 95.3 KiB/172.3 KiB (502.3 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/metadata.rdf\nCompleted 95.3 KiB/172.3 KiB (502.3 KiB/s) with 3 file(s) remaining\rCompleted 98.9 KiB/172.3 KiB (440.0 KiB/s) with 3 file(s) remaining\rupload: contents/Bose2011.ode to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011.ode\nCompleted 98.9 KiB/172.3 KiB (440.0 KiB/s) with 2 file(s) remaining\rCompleted 158.8 KiB/172.3 KiB (632.0 KiB/s) with 2 file(s) remaining\rupload: contents/Bose2011.cps to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011.cps\nCompleted 158.8 KiB/172.3 KiB (632.0 KiB/s) with 1 file(s) remaining\rCompleted 172.3 KiB/172.3 KiB (663.2 KiB/s) with 1 file(s) remaining\rupload: contents/Bose2011-biopax3.owl to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/contents/Bose2011-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.3 KiB/7.3 KiB (58.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f4f195afd5df176211a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:40:44,430 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-dbeb06de-ba44ae1e-8ab7-71fd43-5a64b3/value?select=%5B0%3A19%2C0%3A101%5D&domain=%2Fresults%2F647a5f4f195afd5df176211a (Caused by ResponseError('too many 500 error responses',))\ncreating group /Bose2011.sedml\ncreating dataset /Bose2011.sedml/autogen_report_for_task1, shape: (19, 101), type: float64\ndataset created, uuid: d-dbeb06de-ba44ae1e-8ab7-71fd43-5a64b3, chunk_size: (19, 101)\ncreating dataset /Bose2011.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-dbeb06de-ba44ae1e-8dc3-752ce9-6fa0ba, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Bose2011.sedml\ncreating attribute uri in /Bose2011.sedml\ncreating attribute _type in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute uri in /Bose2011.sedml/autogen_report_for_task1\ncreating attribute _type in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlId in /Bose2011.sedml/plot_1_task1\ncreating attribute sedmlName in /Bose2011.sedml/plot_1_task1\ncreating attribute uri in /Bose2011.sedml/plot_1_task1\ncreate_links: /\ngot link: Bose2011.sedml\ncreate_links: /Bose2011.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Bose2011.sedml/autogen_report_for_task1 to tgt: /Bose2011.sedml/autogen_report_for_task1, shape: (19, 101), type: float64\niterating over chunks for /Bose2011.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-dbeb06de-ba44ae1e-8ab7-71fd43-5a64b3/value?select=%5B0%3A19%2C0%3A101%5D&domain=%2Fresults%2F647a5f4f195afd5df176211a (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Bose2011.sedml/autogen_report_for_task1\nwrite_dataset src: /Bose2011.sedml/plot_1_task1 to tgt: /Bose2011.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Bose2011.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Bose2011.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5f4f195afd5df176211a\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.\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.\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":1.141249,"sedDocuments":[{"location":"Bose2011.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  Bose2011.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      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Bose2011.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":0.733293,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.201659,"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":0.347371,"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":0.06886,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_t","status":"SUCCEEDED"},{"id":"autogen_task1_tau","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_Dx","status":"SUCCEEDED"},{"id":"autogen_task1_Dy","status":"SUCCEEDED"},{"id":"autogen_task1_Dz","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_tumor_system","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_tumor_system","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_effector_cell_against_tumor_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_effector_cell_functioning_against_tumor_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_tumor_detecting_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_tumor_detecting_cell","status":"SUCCEEDED"}]}]}]}