{"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    448      0 --:--:-- --:--:-- --:--:--   448\n\r100 47800  100 47800    0     0   111k      0 --:--:-- --:--:-- --:--:--  111k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nCould not find GLIMDA.\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 (1.21.4) with SciPy (1.7.3)\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 (1.0.0) - 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, 2004-2022  *\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 2.9 KiB/2.9 KiB (45.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/rawLog.txt\nCompleted 7.7 KiB/7.7 KiB (118.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/Macnamara2015_1.sedml/ (stored 0%)\n  adding: outputs/Macnamara2015_1.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 55%)\n  adding: rawLog.txt (deflated 64%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 48.5 KiB/48.5 KiB (553.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/outputs/reports.h5\nCompleted 81 Bytes/75.5 KiB (1.2 KiB/s) with 6 file(s) remaining\rupload: ./Macnamara2015_1.xml-sbml_conversion_errors.txt to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/Macnamara2015_1.xml-sbml_conversion_errors.txt\nCompleted 81 Bytes/75.5 KiB (1.2 KiB/s) with 5 file(s) remaining\rCompleted 22.6 KiB/75.5 KiB (209.2 KiB/s) with 5 file(s) remaining\rupload: ./_pystmptmpbkh1kjqz_parsetab.py to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/_pystmptmpbkh1kjqz_parsetab.py\nCompleted 22.6 KiB/75.5 KiB (209.2 KiB/s) with 4 file(s) remaining\rCompleted 32.3 KiB/75.5 KiB (278.3 KiB/s) with 4 file(s) remaining\rupload: outputs/Macnamara2015_1.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/outputs/Macnamara2015_1.sedml/plot_1_task1.pdf\nCompleted 32.3 KiB/75.5 KiB (278.3 KiB/s) with 3 file(s) remaining\rCompleted 38.6 KiB/75.5 KiB (310.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/outputs/plots.zip\nCompleted 38.6 KiB/75.5 KiB (310.3 KiB/s) with 2 file(s) remaining\rCompleted 42.6 KiB/75.5 KiB (334.2 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/rawLog.txt\nCompleted 42.6 KiB/75.5 KiB (334.2 KiB/s) with 1 file(s) remaining\rCompleted 75.5 KiB/75.5 KiB (522.7 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Macnamara2015_1-biopax2.owl  \n  inflating: contents/Macnamara2015_1-biopax3.owl  \n  inflating: contents/Macnamara2015_1-matlab.m  \n  inflating: contents/Macnamara2015_1-octave.m  \n  inflating: contents/Macnamara2015_1.cps  \n  inflating: contents/Macnamara2015_1.ode  \n  inflating: contents/Macnamara2015_1.sedml  \n  inflating: contents/Macnamara2015_1.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 19.3 KiB/252.3 KiB (284.9 KiB/s) with 12 file(s) remaining\rupload: contents/Macnamara2015_1-biopax3.owl to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1-biopax3.owl\nCompleted 19.3 KiB/252.3 KiB (284.9 KiB/s) with 11 file(s) remaining\rCompleted 25.0 KiB/252.3 KiB (235.2 KiB/s) with 11 file(s) remaining\rupload: contents/Macnamara2015_1-matlab.m to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1-matlab.m\nCompleted 25.0 KiB/252.3 KiB (235.2 KiB/s) with 10 file(s) remaining\rCompleted 43.3 KiB/252.3 KiB (352.9 KiB/s) with 10 file(s) remaining\rupload: contents/Macnamara2015_1.sedml to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1.sedml\nCompleted 43.3 KiB/252.3 KiB (352.9 KiB/s) with 9 file(s) remaining\rCompleted 49.0 KiB/252.3 KiB (367.0 KiB/s) with 9 file(s) remaining\rupload: contents/Macnamara2015_1-octave.m to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1-octave.m\nCompleted 49.0 KiB/252.3 KiB (367.0 KiB/s) with 8 file(s) remaining\rCompleted 49.2 KiB/252.3 KiB (363.6 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/curation_notes.txt\nCompleted 49.2 KiB/252.3 KiB (363.6 KiB/s) with 7 file(s) remaining\rCompleted 50.6 KiB/252.3 KiB (361.6 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/manifest.xml\nCompleted 50.6 KiB/252.3 KiB (361.6 KiB/s) with 6 file(s) remaining\rCompleted 53.7 KiB/252.3 KiB (366.2 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/metadata.rdf\nCompleted 53.7 KiB/252.3 KiB (366.2 KiB/s) with 5 file(s) remaining\rCompleted 76.2 KiB/252.3 KiB (506.3 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/curation_image.png\nCompleted 76.2 KiB/252.3 KiB (506.3 KiB/s) with 4 file(s) remaining\rCompleted 79.8 KiB/252.3 KiB (508.4 KiB/s) with 4 file(s) remaining\rupload: contents/Macnamara2015_1.ode to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1.ode\nCompleted 79.8 KiB/252.3 KiB (508.4 KiB/s) with 3 file(s) remaining\rCompleted 93.4 KiB/252.3 KiB (550.4 KiB/s) with 3 file(s) remaining\rupload: contents/Macnamara2015_1-biopax2.owl to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1-biopax2.owl\nCompleted 93.4 KiB/252.3 KiB (550.4 KiB/s) with 2 file(s) remaining\rCompleted 179.8 KiB/252.3 KiB (1.0 MiB/s) with 2 file(s) remaining \rupload: contents/Macnamara2015_1.cps to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1.cps\nCompleted 179.8 KiB/252.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 252.3 KiB/252.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/Macnamara2015_1.xml to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/contents/Macnamara2015_1.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (142.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f173ee26f4323c900398/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Macnamara2015_1.sedml\ncreating dataset /Macnamara2015_1.sedml/autogen_report_for_task1, shape: (33, 136), type: float64\ndataset created, uuid: d-e94e494f-86e0ae51-ad9b-3d5f33-3e0134, chunk_size: (33, 136)\ncreating dataset /Macnamara2015_1.sedml/plot_1_task1, shape: (3, 136), type: float64\ndataset created, uuid: d-e94e494f-86e0ae51-3683-48adc7-cfbfe7, chunk_size: (3, 136)\ncreating attribute combineArchiveLocation in /Macnamara2015_1.sedml\ncreating attribute uri in /Macnamara2015_1.sedml\ncreating attribute _type in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute uri in /Macnamara2015_1.sedml/autogen_report_for_task1\ncreating attribute _type in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlId in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute sedmlName in /Macnamara2015_1.sedml/plot_1_task1\ncreating attribute uri in /Macnamara2015_1.sedml/plot_1_task1\ncreate_links: /\ngot link: Macnamara2015_1.sedml\ncreate_links: /Macnamara2015_1.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Macnamara2015_1.sedml/autogen_report_for_task1 to tgt: /Macnamara2015_1.sedml/autogen_report_for_task1, shape: (33, 136), type: float64\niterating over chunks for /Macnamara2015_1.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 136, 1))\ndone with dataload for /Macnamara2015_1.sedml/autogen_report_for_task1\nwrite_dataset src: /Macnamara2015_1.sedml/plot_1_task1 to tgt: /Macnamara2015_1.sedml/plot_1_task1, shape: (3, 136), type: float64\niterating over chunks for /Macnamara2015_1.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 136, 1))\ndone with dataload for /Macnamara2015_1.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f173ee26f4323c900398\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":7.163249,"sedDocuments":[{"location":"Macnamara2015_1.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  Macnamara2015_1.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 33 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Macnamara2015_1.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 ...Check SBML support is at action level 2\r\nSBML file is L3V1\r\n\r\n\r\n\r\n*********ERRORS***********\r\n\r\nWARNING: Model is encoded as SBML Level 3, PySCeS only officially supports L2V5.\r\n\r\n*********ERRORS***********\r\n\r\n\r\nPossible errors detected in SBML conversion, Model may be incomplete. Please check the error log file \"Macnamara2015_1.xml-sbml_conversion_errors.txt\" for details.\r\n\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpnlijjlq7/Macnamara2015_1.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['r', 'K', 'dv', 'du', 'hu', 'he', 'hv', 'delta', 'pm', 'm', 'pe', 'de', 'dt', 'w', 'b'] \r\n\r\nFast attribute ignored for reactions:\r\n['tumor_growth', 'tumor_infection', 'tumor_killing', 'infected_tumor_death', 'infected_tumor_killing', 'memory_cell_growth', 'effector_growth', 'effector_death', 'effector_exhaustion', 'virus_burst', 'virus_clearance'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"tumor_growth\" in default compartment\r\nInfo: single compartment model: locating \"tumor_infection\" in default compartment\r\nInfo: single compartment model: locating \"tumor_killing\" in default compartment\r\nInfo: single compartment model: locating \"infected_tumor_death\" in default compartment\r\nInfo: single compartment model: locating \"infected_tumor_killing\" in default compartment\r\nInfo: single compartment model: locating \"memory_cell_growth\" in default compartment\r\nInfo: single compartment model: locating \"effector_growth\" in default compartment\r\nInfo: single compartment model: locating \"effector_death\" in default compartment\r\nInfo: single compartment model: locating \"effector_exhaustion\" in default compartment\r\nInfo: single compartment model: locating \"virus_burst\" in default compartment\r\nInfo: single compartment model: locating \"virus_clearance\" in default compartment\r\nWriting file: /tmp/tmpbkh1kjqz.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpnlijjlq7/Macnamara2015_1.xml\r\nout: /tmp/tmpbkh1kjqz.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpbkh1kjqz.psc loading ..... \r\nParsing file: /tmp/tmpbkh1kjqz.psc\r\nInfo: No reagents have been fixed\r\n \r\nCalculating L matrix . . . . . . .  done.\r\nCalculating K matrix . . . . . . .  done.\r\n \r\nCVODE time for 136 points: 0.17527318000793457\r\n \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":6.864139,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":6.35098,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"pysces.PyscesModel.Simulate"},{"key":"arguments","value":{"cvode_abstol":1e-15,"cvode_mxstep":1000,"cvode_reltol":1e-9,"cvode_return_event_timepoints":false,"cvode_stats":false}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.296071,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.08454,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_dv","status":"SUCCEEDED"},{"id":"autogen_task1_du","status":"SUCCEEDED"},{"id":"autogen_task1_hu","status":"SUCCEEDED"},{"id":"autogen_task1_he","status":"SUCCEEDED"},{"id":"autogen_task1_hv","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_pm","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_pe","status":"SUCCEEDED"},{"id":"autogen_task1_de","status":"SUCCEEDED"},{"id":"autogen_task1_dt","status":"SUCCEEDED"},{"id":"autogen_task1_w","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_tme","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_infection","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_killing","status":"SUCCEEDED"},{"id":"autogen_task1_infected_tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_infected_tumor_killing","status":"SUCCEEDED"},{"id":"autogen_task1_memory_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_effector_growth","status":"SUCCEEDED"},{"id":"autogen_task1_effector_death","status":"SUCCEEDED"},{"id":"autogen_task1_effector_exhaustion","status":"SUCCEEDED"},{"id":"autogen_task1_virus_burst","status":"SUCCEEDED"},{"id":"autogen_task1_virus_clearance","status":"SUCCEEDED"}]}]}]}