{"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    496      0 --:--:-- --:--:-- --:--:--   496\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  517k  100  517k    0     0  1315k      0 --:--:-- --:--:-- --:--:-- 4831k\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 (28.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (64.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/verma2017.sedml/ (stored 0%)\n  adding: outputs/verma2017.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 60%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 40.4 KiB/40.4 KiB (514.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/outputs/reports.h5\nCompleted 24.7 KiB/41.9 KiB (300.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/output.zip\nCompleted 24.7 KiB/41.9 KiB (300.7 KiB/s) with 3 file(s) remaining\rCompleted 30.5 KiB/41.9 KiB (315.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/outputs/plots.zip\nCompleted 30.5 KiB/41.9 KiB (315.3 KiB/s) with 2 file(s) remaining\rCompleted 39.3 KiB/41.9 KiB (378.2 KiB/s) with 2 file(s) remaining\rupload: outputs/verma2017.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/outputs/verma2017.sedml/plot_1_task1.pdf\nCompleted 39.3 KiB/41.9 KiB (378.2 KiB/s) with 1 file(s) remaining\rCompleted 41.9 KiB/41.9 KiB (391.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1605030001-biopax2.owl  \n  inflating: contents/MODEL1605030001-biopax3.owl  \n  inflating: contents/MODEL1605030001-matlab.m  \n  inflating: contents/MODEL1605030001-octave.m  \n  inflating: contents/MODEL1605030001.m  \n  inflating: contents/MODEL1605030001.ode  \n  inflating: contents/MODEL1605030001.pdf  \n  inflating: contents/MODEL1605030001.png  \n  inflating: contents/MODEL1605030001.svg  \n  inflating: contents/MODEL1605030001.vcml  \n  inflating: contents/MODEL1605030001_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/verma2017-biopax2.owl  \n  inflating: contents/verma2017-biopax3.owl  \n  inflating: contents/verma2017-matlab.m  \n  inflating: contents/verma2017-octave.m  \n  inflating: contents/verma2017.cps  \n  inflating: contents/verma2017.ode  \n  inflating: contents/verma2017.sedml  \n  inflating: contents/verma2017.xml  \n  inflating: contents/manifest.xml   \nCompleted 14.2 KiB/1.6 MiB (205.8 KiB/s) with 23 file(s) remaining\rupload: contents/MODEL1605030001-biopax2.owl to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001-biopax2.owl\nCompleted 14.2 KiB/1.6 MiB (205.8 KiB/s) with 22 file(s) remaining\rCompleted 270.2 KiB/1.6 MiB (2.3 MiB/s) with 22 file(s) remaining \rCompleted 279.0 KiB/1.6 MiB (2.3 MiB/s) with 22 file(s) remaining \rupload: contents/MODEL1605030001-matlab.m to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001-matlab.m\nCompleted 279.0 KiB/1.6 MiB (2.3 MiB/s) with 21 file(s) remaining\rCompleted 303.4 KiB/1.6 MiB (2.3 MiB/s) with 21 file(s) remaining\rupload: contents/MODEL1605030001-biopax3.owl to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001-biopax3.owl\nCompleted 303.4 KiB/1.6 MiB (2.3 MiB/s) with 20 file(s) remaining\rCompleted 305.4 KiB/1.6 MiB (2.1 MiB/s) with 20 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/metadata.rdf\nCompleted 305.4 KiB/1.6 MiB (2.1 MiB/s) with 19 file(s) remaining\rCompleted 423.5 KiB/1.6 MiB (2.8 MiB/s) with 19 file(s) remaining\rupload: contents/MODEL1605030001.png to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.png\nCompleted 423.5 KiB/1.6 MiB (2.8 MiB/s) with 18 file(s) remaining\rCompleted 459.6 KiB/1.6 MiB (3.0 MiB/s) with 18 file(s) remaining\rupload: contents/MODEL1605030001.svg to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.svg\nCompleted 459.6 KiB/1.6 MiB (3.0 MiB/s) with 17 file(s) remaining\rCompleted 650.8 KiB/1.6 MiB (4.1 MiB/s) with 17 file(s) remaining\rupload: contents/MODEL1605030001.vcml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.vcml\nCompleted 650.8 KiB/1.6 MiB (4.1 MiB/s) with 16 file(s) remaining\rCompleted 653.4 KiB/1.6 MiB (4.1 MiB/s) with 16 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/manifest.xml\nCompleted 653.4 KiB/1.6 MiB (4.1 MiB/s) with 15 file(s) remaining\rCompleted 666.6 KiB/1.6 MiB (4.1 MiB/s) with 15 file(s) remaining\rupload: contents/MODEL1605030001_url.xml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001_url.xml\nCompleted 666.6 KiB/1.6 MiB (4.1 MiB/s) with 14 file(s) remaining\rCompleted 666.8 KiB/1.6 MiB (3.9 MiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/curation_notes.txt\nCompleted 666.8 KiB/1.6 MiB (3.9 MiB/s) with 13 file(s) remaining\rCompleted 683.8 KiB/1.6 MiB (3.8 MiB/s) with 13 file(s) remaining\rupload: contents/verma2017-biopax2.owl to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017-biopax2.owl\nCompleted 683.8 KiB/1.6 MiB (3.8 MiB/s) with 12 file(s) remaining\rCompleted 711.1 KiB/1.6 MiB (3.8 MiB/s) with 12 file(s) remaining\rupload: contents/verma2017-biopax3.owl to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017-biopax3.owl\nCompleted 711.1 KiB/1.6 MiB (3.8 MiB/s) with 11 file(s) remaining\rCompleted 943.1 KiB/1.6 MiB (4.9 MiB/s) with 11 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/curation_image.png\nCompleted 943.1 KiB/1.6 MiB (4.9 MiB/s) with 10 file(s) remaining\rCompleted 952.3 KiB/1.6 MiB (4.8 MiB/s) with 10 file(s) remaining\rupload: contents/verma2017-matlab.m to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017-matlab.m\nCompleted 952.3 KiB/1.6 MiB (4.8 MiB/s) with 9 file(s) remaining\rCompleted 961.4 KiB/1.6 MiB (4.6 MiB/s) with 9 file(s) remaining\rupload: contents/verma2017-octave.m to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017-octave.m\nCompleted 961.4 KiB/1.6 MiB (4.6 MiB/s) with 8 file(s) remaining\rCompleted 968.2 KiB/1.6 MiB (4.3 MiB/s) with 8 file(s) remaining\rupload: contents/verma2017.ode to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017.ode\nCompleted 968.2 KiB/1.6 MiB (4.3 MiB/s) with 7 file(s) remaining\rCompleted 987.8 KiB/1.6 MiB (4.4 MiB/s) with 7 file(s) remaining\rupload: contents/verma2017.sedml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017.sedml\nCompleted 987.8 KiB/1.6 MiB (4.4 MiB/s) with 6 file(s) remaining\rCompleted 1.2 MiB/1.6 MiB (5.3 MiB/s) with 6 file(s) remaining  \rupload: contents/verma2017.cps to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017.cps\nCompleted 1.2 MiB/1.6 MiB (5.3 MiB/s) with 5 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (6.0 MiB/s) with 5 file(s) remaining\rupload: contents/verma2017.xml to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/verma2017.xml\nCompleted 1.4 MiB/1.6 MiB (6.0 MiB/s) with 4 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (5.9 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1605030001-octave.m to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001-octave.m\nCompleted 1.4 MiB/1.6 MiB (5.9 MiB/s) with 3 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (5.7 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1605030001.m to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.m\nCompleted 1.4 MiB/1.6 MiB (5.7 MiB/s) with 2 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (5.6 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1605030001.ode to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.ode\nCompleted 1.4 MiB/1.6 MiB (5.6 MiB/s) with 1 file(s) remaining\rCompleted 1.6 MiB/1.6 MiB (6.5 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1605030001.pdf to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/contents/MODEL1605030001.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.8 KiB/10.8 KiB (175.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e2449c0d898ffdf72a7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\nERROR 2023-05-26 17:16:54,181 utillib.py:531 ERROR : failed to copy dataset data : HTTPSConnectionPool(host='data.biosimulations.org', port=443): Max retries exceeded with url: /datasets/d-30ca2911-1be3ed40-22b8-996dfe-09a8f9/value?select=%5B0%3A37%2C0%3A101%5D&domain=%2Fresults%2F64711e2449c0d898ffdf72a7 (Caused by ResponseError('too many 500 error responses',))\ncreating group /verma2017.sedml\ncreating dataset /verma2017.sedml/autogen_report_for_task1, shape: (37, 101), type: float64\ndataset created, uuid: d-30ca2911-1be3ed40-22b8-996dfe-09a8f9, chunk_size: (37, 101)\ncreating dataset /verma2017.sedml/plot_1_task1, shape: (2, 101), type: float64\ndataset created, uuid: d-30ca2911-1be3ed40-2adf-0df113-0149ab, chunk_size: (2, 101)\ncreating attribute combineArchiveLocation in /verma2017.sedml\ncreating attribute uri in /verma2017.sedml\ncreating attribute _type in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /verma2017.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /verma2017.sedml/autogen_report_for_task1\ncreating attribute uri in /verma2017.sedml/autogen_report_for_task1\ncreating attribute _type in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlId in /verma2017.sedml/plot_1_task1\ncreating attribute sedmlName in /verma2017.sedml/plot_1_task1\ncreating attribute uri in /verma2017.sedml/plot_1_task1\ncreate_links: /\ngot link: verma2017.sedml\ncreate_links: /verma2017.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /verma2017.sedml/autogen_report_for_task1 to tgt: /verma2017.sedml/autogen_report_for_task1, shape: (37, 101), type: float64\niterating over chunks for /verma2017.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-30ca2911-1be3ed40-22b8-996dfe-09a8f9/value?select=%5B0%3A37%2C0%3A101%5D&domain=%2Fresults%2F64711e2449c0d898ffdf72a7 (Caused by ResponseError('too many 500 error responses',))\ndone with dataload for /verma2017.sedml/autogen_report_for_task1\nwrite_dataset src: /verma2017.sedml/plot_1_task1 to tgt: /verma2017.sedml/plot_1_task1, shape: (2, 101), type: float64\niterating over chunks for /verma2017.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 101, 1))\ndone with dataload for /verma2017.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711e2449c0d898ffdf72a7\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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 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":1.389382,"sedDocuments":[{"location":"verma2017.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  verma2017.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: verma2017.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":0.892729,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.341133,"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":0.302668,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.077583,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_s16","status":"SUCCEEDED"},{"id":"autogen_task1_s2","status":"SUCCEEDED"},{"id":"autogen_task1_s3","status":"SUCCEEDED"},{"id":"autogen_task1_s4","status":"SUCCEEDED"},{"id":"autogen_task1_s14","status":"SUCCEEDED"},{"id":"autogen_task1_s13","status":"SUCCEEDED"},{"id":"autogen_task1_s12","status":"SUCCEEDED"},{"id":"autogen_task1_e_rt","status":"SUCCEEDED"},{"id":"autogen_task1_e_pi","status":"SUCCEEDED"},{"id":"autogen_task1_epi","status":"SUCCEEDED"},{"id":"autogen_task1_omega","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_N1","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_re1","status":"SUCCEEDED"},{"id":"autogen_task1_re3","status":"SUCCEEDED"},{"id":"autogen_task1_re4","status":"SUCCEEDED"},{"id":"autogen_task1_re5","status":"SUCCEEDED"},{"id":"autogen_task1_re7","status":"SUCCEEDED"},{"id":"autogen_task1_re8","status":"SUCCEEDED"},{"id":"autogen_task1_re9","status":"SUCCEEDED"},{"id":"autogen_task1_re11","status":"SUCCEEDED"},{"id":"autogen_task1_re12","status":"SUCCEEDED"},{"id":"autogen_task1_re14","status":"SUCCEEDED"},{"id":"autogen_task1_re15","status":"SUCCEEDED"},{"id":"autogen_task1_re17","status":"SUCCEEDED"},{"id":"autogen_task1_re18","status":"SUCCEEDED"},{"id":"autogen_task1_re20","status":"SUCCEEDED"},{"id":"autogen_task1_re24","status":"SUCCEEDED"},{"id":"autogen_task1_re25","status":"SUCCEEDED"},{"id":"autogen_task1_re26","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_HPV_due_to_HPV_self_proliferating","status":"SUCCEEDED"}]}]}]}