{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    417      0 --:--:-- --:--:-- --:--:--   417\n\r100 47432  100 47432    0     0   101k      0 --:--:-- --:--:-- --:--:--  101k\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 (14.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (28.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/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/Caravagna2010.sedml/ (stored 0%)\n  adding: outputs/Caravagna2010.sedml/plot_1_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 118.8 KiB/118.8 KiB (894.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/outputs/reports.h5\nCompleted 109.2 KiB/133.0 KiB (875.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/output.zip\nCompleted 109.2 KiB/133.0 KiB (875.3 KiB/s) with 3 file(s) remaining\rCompleted 121.3 KiB/133.0 KiB (803.4 KiB/s) with 3 file(s) remaining\rupload: outputs/Caravagna2010.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/outputs/Caravagna2010.sedml/plot_1_task1.pdf\nCompleted 121.3 KiB/133.0 KiB (803.4 KiB/s) with 2 file(s) remaining\rCompleted 130.3 KiB/133.0 KiB (794.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/outputs/plots.zip\nCompleted 130.3 KiB/133.0 KiB (794.2 KiB/s) with 1 file(s) remaining\rCompleted 133.0 KiB/133.0 KiB (761.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Caravagna2010-biopax2.owl  \n  inflating: contents/Caravagna2010-biopax3.owl  \n  inflating: contents/Caravagna2010-matlab.m  \n  inflating: contents/Caravagna2010-octave.m  \n  inflating: contents/Caravagna2010.cps  \n  inflating: contents/Caravagna2010.ode  \n  inflating: contents/Caravagna2010.sedml  \n  inflating: contents/Caravagna2010.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 14.3 KiB/180.7 KiB (127.0 KiB/s) with 12 file(s) remaining\rupload: contents/Caravagna2010-biopax3.owl to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010-biopax3.owl\nCompleted 14.3 KiB/180.7 KiB (127.0 KiB/s) with 11 file(s) remaining\rCompleted 20.4 KiB/180.7 KiB (136.0 KiB/s) with 11 file(s) remaining\rupload: contents/Caravagna2010-matlab.m to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010-matlab.m\nCompleted 20.4 KiB/180.7 KiB (136.0 KiB/s) with 10 file(s) remaining\rCompleted 21.8 KiB/180.7 KiB (133.0 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/manifest.xml\nCompleted 21.8 KiB/180.7 KiB (133.0 KiB/s) with 9 file(s) remaining\rCompleted 32.4 KiB/180.7 KiB (174.3 KiB/s) with 9 file(s) remaining\rupload: contents/Caravagna2010-biopax2.owl to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010-biopax2.owl\nCompleted 32.4 KiB/180.7 KiB (174.3 KiB/s) with 8 file(s) remaining\rCompleted 57.6 KiB/180.7 KiB (299.5 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/curation_image.png\nCompleted 57.6 KiB/180.7 KiB (299.5 KiB/s) with 7 file(s) remaining\rCompleted 63.7 KiB/180.7 KiB (322.0 KiB/s) with 7 file(s) remaining\rupload: contents/Caravagna2010-octave.m to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010-octave.m\nCompleted 63.7 KiB/180.7 KiB (322.0 KiB/s) with 6 file(s) remaining\rCompleted 63.9 KiB/180.7 KiB (318.2 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/curation_notes.txt\nCompleted 63.9 KiB/180.7 KiB (318.2 KiB/s) with 5 file(s) remaining\rCompleted 66.3 KiB/180.7 KiB (326.1 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/metadata.rdf\nCompleted 66.3 KiB/180.7 KiB (326.1 KiB/s) with 4 file(s) remaining\rCompleted 99.0 KiB/180.7 KiB (445.9 KiB/s) with 4 file(s) remaining\rupload: contents/Caravagna2010.xml to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010.xml\nCompleted 99.0 KiB/180.7 KiB (445.9 KiB/s) with 3 file(s) remaining\rCompleted 103.1 KiB/180.7 KiB (454.1 KiB/s) with 3 file(s) remaining\rupload: contents/Caravagna2010.ode to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010.ode\nCompleted 103.1 KiB/180.7 KiB (454.1 KiB/s) with 2 file(s) remaining\rCompleted 118.5 KiB/180.7 KiB (515.1 KiB/s) with 2 file(s) remaining\rupload: contents/Caravagna2010.sedml to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010.sedml\nCompleted 118.5 KiB/180.7 KiB (515.1 KiB/s) with 1 file(s) remaining\rCompleted 180.7 KiB/180.7 KiB (736.2 KiB/s) with 1 file(s) remaining\rupload: contents/Caravagna2010.cps to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/contents/Caravagna2010.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (47.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5ca50fb37cdb9ae7557f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:29:28,023 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-a09c12f6-6fd7c417-65af-56211c-3d0b2f/value?select=%5B0%3A4%2C0%3A1001%5D&domain=%2Fresults%2F647a5ca50fb37cdb9ae7557f (Caused by ResponseError('too many 500 error responses',))\ncreating group /Caravagna2010.sedml\ncreating dataset /Caravagna2010.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\ndataset created, uuid: d-a09c12f6-6fd7c417-a23d-d2d99a-3b107a, chunk_size: (25, 1001)\ncreating dataset /Caravagna2010.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-a09c12f6-6fd7c417-65af-56211c-3d0b2f, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Caravagna2010.sedml\ncreating attribute uri in /Caravagna2010.sedml\ncreating attribute _type in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute uri in /Caravagna2010.sedml/autogen_report_for_task1\ncreating attribute _type in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlId in /Caravagna2010.sedml/plot_1_task1\ncreating attribute sedmlName in /Caravagna2010.sedml/plot_1_task1\ncreating attribute uri in /Caravagna2010.sedml/plot_1_task1\ncreate_links: /\ngot link: Caravagna2010.sedml\ncreate_links: /Caravagna2010.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Caravagna2010.sedml/autogen_report_for_task1 to tgt: /Caravagna2010.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\niterating over chunks for /Caravagna2010.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 1001, 1))\ndone with dataload for /Caravagna2010.sedml/autogen_report_for_task1\nwrite_dataset src: /Caravagna2010.sedml/plot_1_task1 to tgt: /Caravagna2010.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Caravagna2010.sedml/plot_1_task1\nERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-a09c12f6-6fd7c417-65af-56211c-3d0b2f/value?select=%5B0%3A4%2C0%3A1001%5D&domain=%2Fresults%2F647a5ca50fb37cdb9ae7557f (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Caravagna2010.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5ca50fb37cdb9ae7557f\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.312006,"sedDocuments":[{"location":"Caravagna2010.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  Caravagna2010.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Caravagna2010.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":0.891508,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.128035,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.390777,"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":0.24079,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_g2","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_g1","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_g3","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_s1","status":"SUCCEEDED"},{"id":"autogen_task1_s2","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Induction_of_tumor","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_tumor_from_the_system_by_the_action_of_immune_response","status":"SUCCEEDED"},{"id":"autogen_task1_Activation_and_transfer_of_effector_cells_to_the_action_site","status":"SUCCEEDED"},{"id":"autogen_task1_Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor","status":"SUCCEEDED"},{"id":"autogen_task1_Activation_of_interleukin_2","status":"SUCCEEDED"},{"id":"autogen_task1_Deactivation_of_interleukin2","status":"SUCCEEDED"}]}]}]}