{"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    451      0 --:--:-- --:--:-- --:--:--   452\n\r100 33338  100 33338    0     0  77890      0 --:--:-- --:--:-- --:--:-- 77890\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 (15.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (34.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/Wang2019.sedml/ (stored 0%)\n  adding: outputs/Wang2019.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/reports.h5 (deflated 63%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.8 KiB/31.8 KiB (280.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/outputs/reports.h5\nCompleted 21.1 KiB/40.5 KiB (188.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/output.zip\nCompleted 21.1 KiB/40.5 KiB (188.4 KiB/s) with 3 file(s) remaining\rCompleted 31.1 KiB/40.5 KiB (219.4 KiB/s) with 3 file(s) remaining\rupload: outputs/Wang2019.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/outputs/Wang2019.sedml/plot_1_task1.pdf\nCompleted 31.1 KiB/40.5 KiB (219.4 KiB/s) with 2 file(s) remaining\rCompleted 33.7 KiB/40.5 KiB (218.7 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/rawLog.txt\nCompleted 33.7 KiB/40.5 KiB (218.7 KiB/s) with 1 file(s) remaining\rCompleted 40.5 KiB/40.5 KiB (248.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Wang2019-biopax2.owl  \n  inflating: contents/Wang2019-biopax3.owl  \n  inflating: contents/Wang2019-matlab.m  \n  inflating: contents/Wang2019-octave.m  \n  inflating: contents/Wang2019.cps   \n  inflating: contents/Wang2019.ode   \n  inflating: contents/Wang2019.sedml  \n  inflating: contents/Wang2019.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 17.4 KiB/161.8 KiB (162.8 KiB/s) with 12 file(s) remaining\rupload: contents/Wang2019-biopax3.owl to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019-biopax3.owl\nCompleted 17.4 KiB/161.8 KiB (162.8 KiB/s) with 11 file(s) remaining\rCompleted 22.3 KiB/161.8 KiB (154.7 KiB/s) with 11 file(s) remaining\rupload: contents/Wang2019-matlab.m to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019-matlab.m\nCompleted 22.3 KiB/161.8 KiB (154.7 KiB/s) with 10 file(s) remaining\rCompleted 35.0 KiB/161.8 KiB (228.8 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/curation_image.png\nCompleted 35.0 KiB/161.8 KiB (228.8 KiB/s) with 9 file(s) remaining\rCompleted 47.7 KiB/161.8 KiB (290.0 KiB/s) with 9 file(s) remaining\rupload: contents/Wang2019-biopax2.owl to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019-biopax2.owl\nCompleted 47.7 KiB/161.8 KiB (290.0 KiB/s) with 8 file(s) remaining\rCompleted 47.9 KiB/161.8 KiB (279.6 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/curation_notes.txt\nCompleted 47.9 KiB/161.8 KiB (279.6 KiB/s) with 7 file(s) remaining\rCompleted 50.4 KiB/161.8 KiB (281.9 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/metadata.rdf\nCompleted 50.4 KiB/161.8 KiB (281.9 KiB/s) with 6 file(s) remaining\rCompleted 51.7 KiB/161.8 KiB (279.9 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/manifest.xml\nCompleted 51.7 KiB/161.8 KiB (279.9 KiB/s) with 5 file(s) remaining\rCompleted 56.6 KiB/161.8 KiB (290.4 KiB/s) with 5 file(s) remaining\rupload: contents/Wang2019-octave.m to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019-octave.m\nCompleted 56.6 KiB/161.8 KiB (290.4 KiB/s) with 4 file(s) remaining\rCompleted 59.6 KiB/161.8 KiB (298.9 KiB/s) with 4 file(s) remaining\rupload: contents/Wang2019.ode to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019.ode\nCompleted 59.6 KiB/161.8 KiB (298.9 KiB/s) with 3 file(s) remaining\rCompleted 72.6 KiB/161.8 KiB (354.2 KiB/s) with 3 file(s) remaining\rupload: contents/Wang2019.sedml to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019.sedml\nCompleted 72.6 KiB/161.8 KiB (354.2 KiB/s) with 2 file(s) remaining\rCompleted 128.0 KiB/161.8 KiB (599.5 KiB/s) with 2 file(s) remaining\rupload: contents/Wang2019.cps to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019.cps\nCompleted 128.0 KiB/161.8 KiB (599.5 KiB/s) with 1 file(s) remaining\rCompleted 161.8 KiB/161.8 KiB (662.0 KiB/s) with 1 file(s) remaining\rupload: contents/Wang2019.xml to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/contents/Wang2019.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.3 KiB/7.3 KiB (92.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f54195afd5df1762130/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-06-02 17:40:49,461 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-a980f0fc-09817ba1-3d60-238529-1249dc/value?select=%5B0%3A4%2C0%3A101%5D&domain=%2Fresults%2F647a5f54195afd5df1762130 (Caused by ResponseError('too many 500 error responses',))\ncreating group /Wang2019.sedml\ncreating dataset /Wang2019.sedml/autogen_report_for_task1, shape: (22, 101), type: float64\ndataset created, uuid: d-a980f0fc-09817ba1-abf2-37e438-1d14b1, chunk_size: (22, 101)\ncreating dataset /Wang2019.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-a980f0fc-09817ba1-3d60-238529-1249dc, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Wang2019.sedml\ncreating attribute uri in /Wang2019.sedml\ncreating attribute _type in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute uri in /Wang2019.sedml/autogen_report_for_task1\ncreating attribute _type in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlId in /Wang2019.sedml/plot_1_task1\ncreating attribute sedmlName in /Wang2019.sedml/plot_1_task1\ncreating attribute uri in /Wang2019.sedml/plot_1_task1\ncreate_links: /\ngot link: Wang2019.sedml\ncreate_links: /Wang2019.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Wang2019.sedml/autogen_report_for_task1 to tgt: /Wang2019.sedml/autogen_report_for_task1, shape: (22, 101), type: float64\niterating over chunks for /Wang2019.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 22, 1), slice(0, 101, 1))\ndone with dataload for /Wang2019.sedml/autogen_report_for_task1\nwrite_dataset src: /Wang2019.sedml/plot_1_task1 to tgt: /Wang2019.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Wang2019.sedml/plot_1_task1\nERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-a980f0fc-09817ba1-3d60-238529-1249dc/value?select=%5B0%3A4%2C0%3A101%5D&domain=%2Fresults%2F647a5f54195afd5df1762130 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /Wang2019.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5f54195afd5df1762130\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 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 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.\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":1.209245,"sedDocuments":[{"location":"Wang2019.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  Wang2019.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 22 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Wang2019.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":0.767158,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.216041,"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":0.353439,"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":0.071206,"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_I","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_tau","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Uninfected_Cells_Proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_Uninfected_Cells_Infection","status":"SUCCEEDED"},{"id":"autogen_task1_Length_of_Eclipse_Phase","status":"SUCCEEDED"},{"id":"autogen_task1_Cytotoxicity","status":"SUCCEEDED"},{"id":"autogen_task1_Immune_Kill","status":"SUCCEEDED"},{"id":"autogen_task1_Stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_Clearance","status":"SUCCEEDED"}]}]}]}