{"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    243      0 --:--:-- --:--:-- --:--:--   243\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100 13790  100 13790    0     0  20125      0 --:--:-- --:--:-- --:--:--  187k\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 6 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 6\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 (6):\n    Succeeded: 6\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 3.0 KiB/3.0 KiB (19.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 25.2 KiB/25.2 KiB (295.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 87%)\n  adding: outputs/Theinmozhi_2018.sedml/ (stored 0%)\n  adding: outputs/Theinmozhi_2018.sedml/plot_9_task2.pdf (deflated 29%)\n  adding: outputs/Theinmozhi_2018.sedml/plot_10_task2.pdf (deflated 30%)\n  adding: outputs/Theinmozhi_2018.sedml/plot_6_task2.pdf (deflated 30%)\n  adding: outputs/Theinmozhi_2018.sedml/plot_8_task2.pdf (deflated 28%)\n  adding: outputs/Theinmozhi_2018.sedml/plot_7_task2.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 41%)\n  adding: rawLog.txt (deflated 66%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 198.2 KiB/198.2 KiB (451.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 22.6 KiB/322.5 KiB (220.3 KiB/s) with 10 file(s) remaining\rupload: ./_pystmptmpozo0luix_parsetab.py to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/_pystmptmpozo0luix_parsetab.py\nCompleted 22.6 KiB/322.5 KiB (220.3 KiB/s) with 9 file(s) remaining\rCompleted 45.1 KiB/322.5 KiB (365.0 KiB/s) with 9 file(s) remaining\rupload: ./_pystmptmpx0vgpq6l_parsetab.py to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/_pystmptmpx0vgpq6l_parsetab.py\nCompleted 45.1 KiB/322.5 KiB (365.0 KiB/s) with 8 file(s) remaining\rCompleted 55.1 KiB/322.5 KiB (396.2 KiB/s) with 8 file(s) remaining\rupload: outputs/Theinmozhi_2018.sedml/plot_9_task2.pdf to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/Theinmozhi_2018.sedml/plot_9_task2.pdf\nCompleted 55.1 KiB/322.5 KiB (396.2 KiB/s) with 7 file(s) remaining\rCompleted 223.3 KiB/322.5 KiB (1.5 MiB/s) with 7 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/output.zip\nCompleted 223.3 KiB/322.5 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 227.9 KiB/322.5 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/rawLog.txt\nCompleted 227.9 KiB/322.5 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 237.9 KiB/322.5 KiB (631.2 KiB/s) with 5 file(s) remaining\rupload: outputs/Theinmozhi_2018.sedml/plot_10_task2.pdf to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/Theinmozhi_2018.sedml/plot_10_task2.pdf\nCompleted 237.9 KiB/322.5 KiB (631.2 KiB/s) with 4 file(s) remaining\rCompleted 251.3 KiB/322.5 KiB (661.1 KiB/s) with 4 file(s) remaining\rupload: outputs/Theinmozhi_2018.sedml/plot_7_task2.pdf to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/Theinmozhi_2018.sedml/plot_7_task2.pdf\nCompleted 251.3 KiB/322.5 KiB (661.1 KiB/s) with 3 file(s) remaining\rCompleted 264.7 KiB/322.5 KiB (686.8 KiB/s) with 3 file(s) remaining\rupload: outputs/Theinmozhi_2018.sedml/plot_6_task2.pdf to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/Theinmozhi_2018.sedml/plot_6_task2.pdf\nCompleted 264.7 KiB/322.5 KiB (686.8 KiB/s) with 2 file(s) remaining\rCompleted 279.8 KiB/322.5 KiB (659.5 KiB/s) with 2 file(s) remaining\rupload: outputs/Theinmozhi_2018.sedml/plot_8_task2.pdf to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/Theinmozhi_2018.sedml/plot_8_task2.pdf\nCompleted 279.8 KiB/322.5 KiB (659.5 KiB/s) with 1 file(s) remaining\rCompleted 322.5 KiB/322.5 KiB (668.8 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/outputs/plots.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/Theinmozhi_2018.sedml  \n  inflating: contents/Theinmozhi_2018.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 185.5 KiB/252.4 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/Theinmozhi_2018.xml to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/contents/Theinmozhi_2018.xml\nCompleted 185.5 KiB/252.4 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 186.1 KiB/252.4 KiB (496.1 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/contents/manifest.xml\nCompleted 186.1 KiB/252.4 KiB (496.1 KiB/s) with 1 file(s) remaining\rCompleted 252.4 KiB/252.4 KiB (463.3 KiB/s) with 1 file(s) remaining\rupload: contents/Theinmozhi_2018.sedml to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/contents/Theinmozhi_2018.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (105.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868fd2167dc18b5b2486e3/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.\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":5.347431,"sedDocuments":[{"location":"Theinmozhi_2018.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n  Theinmozhi_2018.sedml:\r\n    Tasks (2):\r\n      task1\r\n      task2\r\n    Reports (1):\r\n      autogen_report_for_task2: 120 data sets\r\n    Plots (5):\r\n      plot_10_task2: 1 curves\r\n      plot_6_task2: 1 curves\r\n      plot_7_task2: 1 curves\r\n      plot_8_task2: 2 curves\r\n      plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n  Found 1 tasks and 6 outputs:\r\n    Tasks:\r\n      `task2`\r\n    Outputs:\r\n      `autogen_report_for_task2`\r\n      `plot_10_task2`\r\n      `plot_6_task2`\r\n      `plot_7_task2`\r\n      `plot_8_task2`\r\n      `plot_9_task2`\r\n  Executing task 1: `task2`\r\n    Executing simulation ...Info: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmpx0vgpq6l.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp5q6pk_ra.xml\r\nout: /tmp/tmpx0vgpq6l.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpx0vgpq6l.psc loading ..... \r\nParsing file: /tmp/tmpx0vgpq6l.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" 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\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.15527772903442383\r\n \u001b[34msucceeded\u001b[0m\r\n    Generating 6 outputs ...\r\n      Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 6: `autogen_report_for_task2` ...","duration":4.699213,"tasks":[{"id":"task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Check SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpq4eqm1pv.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\nInfo: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmpozo0luix.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpq4eqm1pv.xml\r\nout: /tmp/tmpozo0luix.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpozo0luix.psc loading ..... \r\nParsing file: /tmp/tmpozo0luix.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" 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\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.175856351852417\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmp5q6pk_ra.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\n","duration":3.161568,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"plot_6_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.308422,"curves":[{"id":"p1_curve_1_task2","status":"SUCCEEDED"}]},{"id":"plot_7_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.15776,"curves":[{"id":"p2_curve_1_task2","status":"SUCCEEDED"}]},{"id":"plot_8_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.141906,"curves":[{"id":"p3_curve_1_task2","status":"SUCCEEDED"},{"id":"p3_curve_2_task2","status":"SUCCEEDED"}]},{"id":"plot_9_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.142771,"curves":[{"id":"p4_curve_1_task2","status":"SUCCEEDED"}]},{"id":"plot_10_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.123865,"curves":[{"id":"p5_curve_1_task2","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.197629,"dataSets":[{"id":"autogen_time_for_task2","status":"SUCCEEDED"},{"id":"autogen_task2_perc_PI3K_free","status":"SUCCEEDED"},{"id":"autogen_task2_perc_ZAP70_free","status":"SUCCEEDED"},{"id":"autogen_task2_perc_LCK_active","status":"SUCCEEDED"},{"id":"autogen_task2_perc_LCK_inactive","status":"SUCCEEDED"},{"id":"autogen_task2_SLP76a","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70a2","status":"SUCCEEDED"},{"id":"autogen_task2_LCKi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKya","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyiya","status":"SUCCEEDED"},{"id":"autogen_task2_LCKpi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKt","status":"SUCCEEDED"},{"id":"autogen_task2_LCKactive","status":"SUCCEEDED"},{"id":"autogen_task2_PD1","status":"SUCCEEDED"},{"id":"autogen_task2_PD1p1","status":"SUCCEEDED"},{"id":"autogen_task2_PD1p2","status":"SUCCEEDED"},{"id":"autogen_task2_CP1","status":"SUCCEEDED"},{"id":"autogen_task2_SHP2","status":"SUCCEEDED"},{"id":"autogen_task2_CP2","status":"SUCCEEDED"},{"id":"autogen_task2_CPactive","status":"SUCCEEDED"},{"id":"autogen_task2_CD28a","status":"SUCCEEDED"},{"id":"autogen_task2_CD28i","status":"SUCCEEDED"},{"id":"autogen_task2_PI3K","status":"SUCCEEDED"},{"id":"autogen_task2_PI3Kb","status":"SUCCEEDED"},{"id":"autogen_task2_CD28t","status":"SUCCEEDED"},{"id":"autogen_task2_CD3a","status":"SUCCEEDED"},{"id":"autogen_task2_CD3i","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70a1","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70i","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70","status":"SUCCEEDED"},{"id":"autogen_task2_PI3Kt","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70t","status":"SUCCEEDED"},{"id":"autogen_task2_LATa","status":"SUCCEEDED"},{"id":"autogen_task2_LATi","status":"SUCCEEDED"},{"id":"autogen_task2_LATt","status":"SUCCEEDED"},{"id":"autogen_task2_GADS","status":"SUCCEEDED"},{"id":"autogen_task2_SLP76","status":"SUCCEEDED"},{"id":"autogen_task2_SLP76i","status":"SUCCEEDED"},{"id":"autogen_task2_GADSt","status":"SUCCEEDED"},{"id":"autogen_task2_SLP76t","status":"SUCCEEDED"},{"id":"autogen_task2_CD3t","status":"SUCCEEDED"},{"id":"autogen_task2_GADSa","status":"SUCCEEDED"},{"id":"autogen_task2_LCKinactive","status":"SUCCEEDED"},{"id":"autogen_task2_Kdpa_yiya","status":"SUCCEEDED"},{"id":"autogen_task2_Kdpi_yi","status":"SUCCEEDED"},{"id":"autogen_task2_Kdpi_yiya","status":"SUCCEEDED"},{"id":"autogen_task2_Kdpa_ya","status":"SUCCEEDED"},{"id":"autogen_task2_Kdpa_pi","status":"SUCCEEDED"},{"id":"autogen_task2_Kpi_i","status":"SUCCEEDED"},{"id":"autogen_task2_Kpi_ya","status":"SUCCEEDED"},{"id":"autogen_task2_Kpa_i","status":"SUCCEEDED"},{"id":"autogen_task2_Kpa_yi","status":"SUCCEEDED"},{"id":"autogen_task2_k","status":"SUCCEEDED"},{"id":"autogen_task2_Kp_pd1","status":"SUCCEEDED"},{"id":"autogen_task2_KMp_pd1","status":"SUCCEEDED"},{"id":"autogen_task2_Ka_shp","status":"SUCCEEDED"},{"id":"autogen_task2_Kd1_shp","status":"SUCCEEDED"},{"id":"autogen_task2_Kd2_shp","status":"SUCCEEDED"},{"id":"autogen_task2_Kdp_cp2","status":"SUCCEEDED"},{"id":"autogen_task2_Kp_cd28","status":"SUCCEEDED"},{"id":"autogen_task2_KMp_cd28","status":"SUCCEEDED"},{"id":"autogen_task2_Kdp_cd28","status":"SUCCEEDED"},{"id":"autogen_task2_KMdp_cd28","status":"SUCCEEDED"},{"id":"autogen_task2_Ka_pi3k","status":"SUCCEEDED"},{"id":"autogen_task2_Kd_pi3k","status":"SUCCEEDED"},{"id":"autogen_task2_Kp_cd3","status":"SUCCEEDED"},{"id":"autogen_task2_KMp_cd3","status":"SUCCEEDED"},{"id":"autogen_task2_Kdp_cd3","status":"SUCCEEDED"},{"id":"autogen_task2_KMdp_cd3","status":"SUCCEEDED"},{"id":"autogen_task2_Ka_zap","status":"SUCCEEDED"},{"id":"autogen_task2_Kd_zap","status":"SUCCEEDED"},{"id":"autogen_task2_Kp1_zap","status":"SUCCEEDED"},{"id":"autogen_task2_Kp2_zap","status":"SUCCEEDED"},{"id":"autogen_task2_Kp_lat","status":"SUCCEEDED"},{"id":"autogen_task2_Ka_gads","status":"SUCCEEDED"},{"id":"autogen_task2_Kd_gads","status":"SUCCEEDED"},{"id":"autogen_task2_Ka_slp","status":"SUCCEEDED"},{"id":"autogen_task2_Kd_slp","status":"SUCCEEDED"},{"id":"autogen_task2_Kp_slp","status":"SUCCEEDED"},{"id":"autogen_task2_perc_SHP2_bound","status":"SUCCEEDED"},{"id":"autogen_task2_CD3z_phosphorylated","status":"SUCCEEDED"},{"id":"autogen_task2_CD28_phosphorylated","status":"SUCCEEDED"},{"id":"autogen_task2_perc_SHP2_free","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70_phos_Y315","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70_phos_Y93","status":"SUCCEEDED"},{"id":"autogen_task2_LCK_phos_Y505","status":"SUCCEEDED"},{"id":"autogen_task2_LCK_phos_Y394","status":"SUCCEEDED"},{"id":"autogen_task2_LAT_phosphorylated","status":"SUCCEEDED"},{"id":"autogen_task2_LCK_switch","status":"SUCCEEDED"},{"id":"autogen_task2_ModelValue_0","status":"SUCCEEDED"},{"id":"autogen_task2_Cell","status":"SUCCEEDED"},{"id":"autogen_task2_LCK_P_LCKyi_inh","status":"SUCCEEDED"},{"id":"autogen_task2_LCK_P_LCKya_act","status":"SUCCEEDED"},{"id":"autogen_task2_LCKya_P_LCKyiya_act","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyi_P_LCKpi_inh","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyiya_DP_LCKyi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKya_DP_LCKi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyi_DP_LCKi","status":"SUCCEEDED"},{"id":"autogen_task2_LCKyiya_DP_LCKya","status":"SUCCEEDED"},{"id":"autogen_task2_LCKpi_DP_LCKyi","status":"SUCCEEDED"},{"id":"autogen_task2_PD1_P_PD1p1_act","status":"SUCCEEDED"},{"id":"autogen_task2_PD1p1_P_PD1p2_act","status":"SUCCEEDED"},{"id":"autogen_task2_PD1p1_Bd_SHP2","status":"SUCCEEDED"},{"id":"autogen_task2_PD1p2_Bd_SHP2","status":"SUCCEEDED"},{"id":"autogen_task2_CP2_Diss_SHP2_PD1p1","status":"SUCCEEDED"},{"id":"autogen_task2_CP2_DP_CP1","status":"SUCCEEDED"},{"id":"autogen_task2_CP1_Diss_PD1_SHP2","status":"SUCCEEDED"},{"id":"autogen_task2_CD28i_P_CD28a","status":"SUCCEEDED"},{"id":"autogen_task2_CD28a_DP_CD28i","status":"SUCCEEDED"},{"id":"autogen_task2_CD28a_Bd_PI3K","status":"SUCCEEDED"},{"id":"autogen_task2_CD3i_P_CD3a","status":"SUCCEEDED"},{"id":"autogen_task2_CD3a_DP_CD3i","status":"SUCCEEDED"},{"id":"autogen_task2_CD3a_Bd_ZAP70","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70i_P_ZAP70a1","status":"SUCCEEDED"},{"id":"autogen_task2_ZAP70a1_P_ZAP70a2","status":"SUCCEEDED"},{"id":"autogen_task2_LATi_P_LATa","status":"SUCCEEDED"},{"id":"autogen_task2_LATa_Bd_GADS","status":"SUCCEEDED"},{"id":"autogen_task2_GADSa_Bd_SLP76","status":"SUCCEEDED"},{"id":"autogen_task2_SLP76i_P_SLC76a","status":"SUCCEEDED"}]}]}]}