{"status":"FAILED","exception":{"type":"ValueError","message":"`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n    - Output `autogen_plot3` is invalid.\n      - Plot must have at least one curve."},"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    473      0 --:--:-- --:--:-- --:--:--   474\n\r100  5669  100  5669    0     0  13786      0 --:--:-- --:--:-- --:--:-- 13786\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nlibtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified                          in the user configuration file, set \"matplotlib_backend = <backend>\" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems   *\r\n*                http://pysces.sourceforge.net                        *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024  *\r\n* Triple-J Group for Molecular Cell Physiology                        *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL         *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see     *\r\n* LICENCE.txt (supplied with this release) for details                *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *\r\n***********************************************************************\r\n`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n    - Output `autogen_plot3` is invalid.\n      - Plot must have at least one curve.\nsrun: error: xanadu-73: task 0: Exited with exit code 1\nsrun: Terminating job step 8658191.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.7 KiB/2.7 KiB (29.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 1.8 KiB/1.8 KiB (21.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 51%)\n  adding: rawLog.txt (deflated 62%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 2.6 KiB/6.3 KiB (22.2 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/output.zip\nCompleted 2.6 KiB/6.3 KiB (22.2 KiB/s) with 1 file(s) remaining\rCompleted 6.3 KiB/6.3 KiB (39.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/BIOMD0000000138_url.sedml  \n  inflating: contents/BIOMD0000000138_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 23.0 KiB/43.3 KiB (258.3 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000138_url.sedml to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/contents/BIOMD0000000138_url.sedml\nCompleted 23.0 KiB/43.3 KiB (258.3 KiB/s) with 2 file(s) remaining\rCompleted 42.7 KiB/43.3 KiB (361.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000138_url.xml to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/contents/BIOMD0000000138_url.xml\nCompleted 42.7 KiB/43.3 KiB (361.0 KiB/s) with 1 file(s) remaining\rCompleted 43.3 KiB/43.3 KiB (133.1 KiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.3 KiB/5.3 KiB (53.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5c1261553b9bc253dcc/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;32mRetrieve 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.\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;31mPost the SED-ML file to the API ... failed due to: Failed to post SED-ML specs:\nThere was an error uploading the SED-ML specifications to the API.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":0.202896,"sedDocuments":[]}