{"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    466      0 --:--:-- --:--:-- --:--:--   466\r100   139  100   139    0     0    458      0 --:--:-- --:--:-- --:--:--   457\n\r100  2508  100  2508    0     0   6053      0 --:--:-- --:--:-- --:--:--  6053\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 (17.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 2.5 KiB/2.5 KiB (25.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 61%)\n  adding: outputs/tmp669222/ (stored 0%)\n  adding: outputs/tmp669222/d1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/407.8 KiB (7.3 MiB/s) with 1 file(s) remaining\rCompleted 407.8 KiB/407.8 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/384.3 KiB (4.3 MiB/s) with 4 file(s) remaining\rCompleted 265.8 KiB/384.3 KiB (3.1 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/outputs/plots.zip\nCompleted 265.8 KiB/384.3 KiB (3.1 MiB/s) with 3 file(s) remaining\rCompleted 279.2 KiB/384.3 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: outputs/tmp669222/d1.pdf to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/outputs/tmp669222/d1.pdf\nCompleted 279.2 KiB/384.3 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 282.1 KiB/384.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/rawLog.txt\nCompleted 282.1 KiB/384.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 384.3 KiB/384.3 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/output.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/tmp669222      \n  inflating: contents/LEMS_NML2_Ex9_FN.sbml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 3.6 KiB/8.5 KiB (34.4 KiB/s) with 3 file(s) remaining\rupload: contents/LEMS_NML2_Ex9_FN.sbml to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/contents/LEMS_NML2_Ex9_FN.sbml\nCompleted 3.6 KiB/8.5 KiB (34.4 KiB/s) with 2 file(s) remaining\rCompleted 7.8 KiB/8.5 KiB (69.7 KiB/s) with 2 file(s) remaining\rupload: contents/tmp669222 to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/contents/tmp669222\nCompleted 7.8 KiB/8.5 KiB (69.7 KiB/s) with 1 file(s) remaining\rCompleted 8.5 KiB/8.5 KiB (71.2 KiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.1 KiB/5.1 KiB (57.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67224854953bc3bf105ef4f7/rawLog.txt\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.\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":23.418593,"sedDocuments":[{"location":"tmp669222","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  tmp669222:\r\n    Tasks (1):\r\n      sim1_net1\r\n    Reports (1):\r\n      ex9: 3 data sets\r\n    Plots (1):\r\n      d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp669222 ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `sim1_net1`\r\n    Outputs:\r\n      `d1`\r\n      `ex9`\r\n  Executing task 1: `sim1_net1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `ex9` ...","duration":23.049864,"tasks":[{"id":"sim1_net1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"2024-10-30 10:53:37.384 - amici.swig_wrappers - ERROR - [OTHER] AMICI simulation failed: Reached maximum number of steps 10000 before reaching tout at t=99.66.\r\n2024-10-30 10:53:37.385 - amici.swig_wrappers - DEBUG - [BACKTRACE] The previous error occurred at:\r\n2       0x7ffff3462a8b /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0xb5a8b) [0x7ffff3462a8b]\r\n3       0x7ffff3556262 amici::Solver::run(double) const + 34\r\n4       0x7ffff358e5d0 amici::ForwardProblem::workForwardProblem() + 1728\r\n5       0x7ffff3542763 amici::runAmiciSimulation(amici::Solver&, amici::ExpData const*, amici::Model&, bool) + 435\r\n6       0x7ffff34ec280 /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0x13f\r\n","duration":21.809379,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.swig_wrappers.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"d1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.842209,"curves":[{"id":"curve_V","status":"SUCCEEDED"},{"id":"curve_W","status":"SUCCEEDED"}]},{"id":"ex9","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.315764,"dataSets":[{"id":"ex9_time","status":"SUCCEEDED"},{"id":"ex9_V","status":"SUCCEEDED"},{"id":"ex9_W","status":"SUCCEEDED"}]}]}]}