{"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    469      0 --:--:-- --:--:-- --:--:--   471\n\r  7  8231    7   603    0     0   1442      0  0:00:05 --:--:--  0:00:05  1442\r100  8231  100  8231    0     0  19311      0 --:--:-- --:--:-- --:--:--  931k\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 \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 3.0 KiB/3.0 KiB (40.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 9.7 KiB/9.7 KiB (90.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/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/BIOMD0000000001_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 65%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/324.1 KiB (6.2 MiB/s) with 1 file(s) remaining\rCompleted 324.1 KiB/324.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 22.6 KiB/346.2 KiB (252.1 KiB/s) with 5 file(s) remaining\rupload: ./_pystmptmpnk0gukmy_parsetab.py to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/_pystmptmpnk0gukmy_parsetab.py\nCompleted 22.6 KiB/346.2 KiB (252.1 KiB/s) with 4 file(s) remaining\rCompleted 33.5 KiB/346.2 KiB (302.3 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf\nCompleted 33.5 KiB/346.2 KiB (302.3 KiB/s) with 3 file(s) remaining\rCompleted 289.5 KiB/346.2 KiB (2.5 MiB/s) with 3 file(s) remaining \rCompleted 297.0 KiB/346.2 KiB (2.2 MiB/s) with 3 file(s) remaining \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/outputs/plots.zip\nCompleted 297.0 KiB/346.2 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 301.3 KiB/346.2 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/rawLog.txt\nCompleted 301.3 KiB/346.2 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 346.2 KiB/346.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/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/BIOMD0000000001_url.sedml  \n  inflating: contents/BIOMD0000000001_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 35.4 KiB/85.3 KiB (260.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000001_url.sedml to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/contents/BIOMD0000000001_url.sedml\nCompleted 35.4 KiB/85.3 KiB (260.5 KiB/s) with 2 file(s) remaining\rCompleted 36.0 KiB/85.3 KiB (248.2 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/contents/manifest.xml\nCompleted 36.0 KiB/85.3 KiB (248.2 KiB/s) with 1 file(s) remaining\rCompleted 85.3 KiB/85.3 KiB (156.2 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000001_url.xml to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/contents/BIOMD0000000001_url.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 6.9 KiB/6.9 KiB (73.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4bbef911d5d452598e2/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 SED-ML file in the COMBINE archive ... 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.\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":1.614328,"sedDocuments":[{"location":"BIOMD0000000001_url.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  BIOMD0000000001_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 66 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpnk0gukmy.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpef1rqg3q.xml\r\nout: /tmp/tmpnk0gukmy.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpnk0gukmy.psc loading ..... \r\nParsing file: /tmp/tmpnk0gukmy.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . .  done.\r\nCalculating K matrix . . . . . . .  done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.07132816314697266\r\n \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":1.296853,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.31707,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"pysces.PyscesModel.Simulate"},{"key":"arguments","value":{"cvode_abstol":1e-9,"cvode_access_solver":true,"cvode_h0":0,"cvode_hmax":0,"cvode_hmin":0,"cvode_mxord":5,"cvode_mxstep":5000,"cvode_reltol":1e-9,"cvode_return_event_timepoints":false,"cvode_stats":false,"cvode_track_assignment_rules":true}}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.354192,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_task1_IL","status":"SUCCEEDED"},{"id":"autogen_task1_AL","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_BL","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_task1_DL","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_ALL","status":"SUCCEEDED"},{"id":"autogen_task1_kf_0","status":"SUCCEEDED"},{"id":"autogen_task1_kr_0","status":"SUCCEEDED"},{"id":"autogen_task1_kf_1","status":"SUCCEEDED"},{"id":"autogen_task1_kr_1","status":"SUCCEEDED"},{"id":"autogen_task1_kf_2","status":"SUCCEEDED"},{"id":"autogen_task1_kr_2","status":"SUCCEEDED"},{"id":"autogen_task1_kf_3","status":"SUCCEEDED"},{"id":"autogen_task1_kr_3","status":"SUCCEEDED"},{"id":"autogen_task1_kf_4","status":"SUCCEEDED"},{"id":"autogen_task1_kr_4","status":"SUCCEEDED"},{"id":"autogen_task1_kf_5","status":"SUCCEEDED"},{"id":"autogen_task1_kr_5","status":"SUCCEEDED"},{"id":"autogen_task1_kf_6","status":"SUCCEEDED"},{"id":"autogen_task1_kr_6","status":"SUCCEEDED"},{"id":"autogen_task1_kf_7","status":"SUCCEEDED"},{"id":"autogen_task1_kr_7","status":"SUCCEEDED"},{"id":"autogen_task1_kf_8","status":"SUCCEEDED"},{"id":"autogen_task1_kr_8","status":"SUCCEEDED"},{"id":"autogen_task1_kf_9","status":"SUCCEEDED"},{"id":"autogen_task1_kr_9","status":"SUCCEEDED"},{"id":"autogen_task1_kf_10","status":"SUCCEEDED"},{"id":"autogen_task1_kr_10","status":"SUCCEEDED"},{"id":"autogen_task1_kf_11","status":"SUCCEEDED"},{"id":"autogen_task1_kr_11","status":"SUCCEEDED"},{"id":"autogen_task1_kf_12","status":"SUCCEEDED"},{"id":"autogen_task1_kr_12","status":"SUCCEEDED"},{"id":"autogen_task1_kf_13","status":"SUCCEEDED"},{"id":"autogen_task1_kr_13","status":"SUCCEEDED"},{"id":"autogen_task1_kf_14","status":"SUCCEEDED"},{"id":"autogen_task1_kr_14","status":"SUCCEEDED"},{"id":"autogen_task1_kf_15","status":"SUCCEEDED"},{"id":"autogen_task1_kr_15","status":"SUCCEEDED"},{"id":"autogen_task1_kf_16","status":"SUCCEEDED"},{"id":"autogen_task1_kr_16","status":"SUCCEEDED"},{"id":"autogen_task1_t2","status":"SUCCEEDED"},{"id":"autogen_task1_comp1","status":"SUCCEEDED"},{"id":"autogen_task1_React0","status":"SUCCEEDED"},{"id":"autogen_task1_React1","status":"SUCCEEDED"},{"id":"autogen_task1_React2","status":"SUCCEEDED"},{"id":"autogen_task1_React3","status":"SUCCEEDED"},{"id":"autogen_task1_React4","status":"SUCCEEDED"},{"id":"autogen_task1_React5","status":"SUCCEEDED"},{"id":"autogen_task1_React6","status":"SUCCEEDED"},{"id":"autogen_task1_React7","status":"SUCCEEDED"},{"id":"autogen_task1_React8","status":"SUCCEEDED"},{"id":"autogen_task1_React9","status":"SUCCEEDED"},{"id":"autogen_task1_React10","status":"SUCCEEDED"},{"id":"autogen_task1_React11","status":"SUCCEEDED"},{"id":"autogen_task1_React12","status":"SUCCEEDED"},{"id":"autogen_task1_React13","status":"SUCCEEDED"},{"id":"autogen_task1_React14","status":"SUCCEEDED"},{"id":"autogen_task1_React15","status":"SUCCEEDED"},{"id":"autogen_task1_React16","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.457523,"curves":[{"id":"autogen_curve_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_B","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ALL","status":"SUCCEEDED"}]}]}]}