{"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    462      0 --:--:-- --:--:-- --:--:--   463\n\r100  328k  100  328k    0     0   744k      0 --:--:-- --:--:-- --:--:--  744k\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 (12.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (23.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/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/Khajanchi2015.sedml/ (stored 0%)\n  adding: outputs/Khajanchi2015.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 70%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 28.6 KiB/28.6 KiB (121.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/outputs/reports.h5\nCompleted 18.8 KiB/39.9 KiB (208.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/output.zip\nCompleted 18.8 KiB/39.9 KiB (208.2 KiB/s) with 3 file(s) remaining\rCompleted 26.5 KiB/39.9 KiB (163.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/outputs/plots.zip\nCompleted 26.5 KiB/39.9 KiB (163.6 KiB/s) with 2 file(s) remaining\rCompleted 29.1 KiB/39.9 KiB (178.0 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/rawLog.txt\nCompleted 29.1 KiB/39.9 KiB (178.0 KiB/s) with 1 file(s) remaining\rCompleted 39.9 KiB/39.9 KiB (222.8 KiB/s) with 1 file(s) remaining\rupload: outputs/Khajanchi2015.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/outputs/Khajanchi2015.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Khajanchi2015-biopax2.owl  \n  inflating: contents/Khajanchi2015-biopax3.owl  \n  inflating: contents/Khajanchi2015-matlab.m  \n  inflating: contents/Khajanchi2015-octave.m  \n  inflating: contents/Khajanchi2015.cps  \n  inflating: contents/Khajanchi2015.ode  \n  inflating: contents/Khajanchi2015.sedml  \n  inflating: contents/Khajanchi2015.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 10.3 KiB/497.1 KiB (94.5 KiB/s) with 12 file(s) remaining\rupload: contents/Khajanchi2015-biopax3.owl to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015-biopax3.owl\nCompleted 10.3 KiB/497.1 KiB (94.5 KiB/s) with 11 file(s) remaining\rCompleted 266.3 KiB/497.1 KiB (1.8 MiB/s) with 11 file(s) remaining\rCompleted 274.3 KiB/497.1 KiB (1.7 MiB/s) with 11 file(s) remaining\rupload: contents/Khajanchi2015-biopax2.owl to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015-biopax2.owl\nCompleted 274.3 KiB/497.1 KiB (1.7 MiB/s) with 10 file(s) remaining\rCompleted 278.9 KiB/497.1 KiB (1.7 MiB/s) with 10 file(s) remaining\rupload: contents/Khajanchi2015-matlab.m to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015-matlab.m\nCompleted 278.9 KiB/497.1 KiB (1.7 MiB/s) with 9 file(s) remaining\rCompleted 283.5 KiB/497.1 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/Khajanchi2015-octave.m to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015-octave.m\nCompleted 283.5 KiB/497.1 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 284.8 KiB/497.1 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/manifest.xml\nCompleted 284.8 KiB/497.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 288.5 KiB/497.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/metadata.rdf\nCompleted 288.5 KiB/497.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 291.3 KiB/497.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/Khajanchi2015.ode to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015.ode\nCompleted 291.3 KiB/497.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 411.7 KiB/497.1 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/curation_image.png\nCompleted 411.7 KiB/497.1 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 462.6 KiB/497.1 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/Khajanchi2015.cps to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015.cps\nCompleted 462.6 KiB/497.1 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 473.6 KiB/497.1 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/Khajanchi2015.sedml to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015.sedml\nCompleted 473.6 KiB/497.1 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 497.0 KiB/497.1 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/Khajanchi2015.xml to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/Khajanchi2015.xml\nCompleted 497.0 KiB/497.1 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 497.1 KiB/497.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (79.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9e0fb37cdb9ae75568/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:29:29,085 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-71d89c45-cebb82ef-1b6d-de82cf-b39433/value?select=%5B0%3A18%2C0%3A101%5D&domain=%2Fresults%2F647a5c9e0fb37cdb9ae75568 (Caused by ResponseError('too many 500 error responses',))\ncreating group /Khajanchi2015.sedml\ncreating dataset /Khajanchi2015.sedml/autogen_report_for_task1, shape: (18, 101), type: float64\ndataset created, uuid: d-71d89c45-cebb82ef-1b6d-de82cf-b39433, chunk_size: (18, 101)\ncreating dataset /Khajanchi2015.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-71d89c45-cebb82ef-b903-f81184-99480c, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Khajanchi2015.sedml\ncreating attribute uri in /Khajanchi2015.sedml\ncreating attribute _type in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute uri in /Khajanchi2015.sedml/autogen_report_for_task1\ncreating attribute _type in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlId in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute sedmlName in /Khajanchi2015.sedml/plot_1_task1\ncreating attribute uri in /Khajanchi2015.sedml/plot_1_task1\ncreate_links: /\ngot link: Khajanchi2015.sedml\ncreate_links: /Khajanchi2015.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Khajanchi2015.sedml/autogen_report_for_task1 to tgt: /Khajanchi2015.sedml/autogen_report_for_task1, shape: (18, 101), type: float64\niterating over chunks for /Khajanchi2015.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-71d89c45-cebb82ef-1b6d-de82cf-b39433/value?select=%5B0%3A18%2C0%3A101%5D&domain=%2Fresults%2F647a5c9e0fb37cdb9ae75568 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Khajanchi2015.sedml/autogen_report_for_task1\nwrite_dataset src: /Khajanchi2015.sedml/plot_1_task1 to tgt: /Khajanchi2015.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Khajanchi2015.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Khajanchi2015.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5c9e0fb37cdb9ae75568\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 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":1.169759,"sedDocuments":[{"location":"Khajanchi2015.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  Khajanchi2015.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 18 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Khajanchi2015.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":0.7674,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.202211,"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":0.36497,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.072041,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_e1","status":"SUCCEEDED"},{"id":"autogen_task1_e2","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Fomation_of_activated_immune_effector_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_activated_tumor_immune_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_tumor_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_tumor_cell","status":"SUCCEEDED"}]}]}]}