{"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    454      0 --:--:-- --:--:-- --:--:--   455\n\r100  187k  100  187k    0     0   434k      0 --:--:-- --:--:-- --:--:--  434k\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 3 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 3\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 (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.9 KiB/2.9 KiB (45.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/rawLog.txt\nCompleted 7.3 KiB/7.3 KiB (111.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/Cui2008.sedml/ (stored 0%)\n  adding: outputs/Cui2008.sedml/plot_2_task1.pdf (deflated 34%)\n  adding: outputs/Cui2008.sedml/plot_1_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 37%)\n  adding: rawLog.txt (deflated 64%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 84.1 KiB/84.1 KiB (1012.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/outputs/reports.h5\nCompleted 81 Bytes/123.7 KiB (1.3 KiB/s) with 7 file(s) remaining\rupload: ./Cui2008.xml-sbml_conversion_errors.txt to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/Cui2008.xml-sbml_conversion_errors.txt\nCompleted 81 Bytes/123.7 KiB (1.3 KiB/s) with 6 file(s) remaining\rCompleted 8.7 KiB/123.7 KiB (78.3 KiB/s) with 6 file(s) remaining\rupload: outputs/Cui2008.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/outputs/Cui2008.sedml/plot_1_task1.pdf\nCompleted 8.7 KiB/123.7 KiB (78.3 KiB/s) with 5 file(s) remaining\rCompleted 17.4 KiB/123.7 KiB (147.0 KiB/s) with 5 file(s) remaining\rupload: outputs/Cui2008.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/outputs/Cui2008.sedml/plot_2_task1.pdf\nCompleted 17.4 KiB/123.7 KiB (147.0 KiB/s) with 4 file(s) remaining\rCompleted 28.3 KiB/123.7 KiB (237.5 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/outputs/plots.zip\nCompleted 28.3 KiB/123.7 KiB (237.5 KiB/s) with 3 file(s) remaining\rCompleted 97.1 KiB/123.7 KiB (779.4 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/output.zip\nCompleted 97.1 KiB/123.7 KiB (779.4 KiB/s) with 2 file(s) remaining\rCompleted 119.7 KiB/123.7 KiB (936.4 KiB/s) with 2 file(s) remaining\rupload: ./_pystmptmpn6ohz40z_parsetab.py to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/_pystmptmpn6ohz40z_parsetab.py\nCompleted 119.7 KiB/123.7 KiB (936.4 KiB/s) with 1 file(s) remaining\rCompleted 123.7 KiB/123.7 KiB (899.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Cui2008.cps    \n  inflating: contents/Cui2008.sedml  \n  inflating: contents/Cui2008.xml    \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 14.3 KiB/414.1 KiB (212.4 KiB/s) with 7 file(s) remaining\rupload: contents/Cui2008.sedml to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/Cui2008.sedml\nCompleted 14.3 KiB/414.1 KiB (212.4 KiB/s) with 6 file(s) remaining\rCompleted 126.5 KiB/414.1 KiB (1.0 MiB/s) with 6 file(s) remaining \rupload: contents/Cui2008.cps to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/Cui2008.cps\nCompleted 126.5 KiB/414.1 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 127.3 KiB/414.1 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/manifest.xml\nCompleted 127.3 KiB/414.1 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 127.3 KiB/414.1 KiB (1007.7 KiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/curation_notes.txt\nCompleted 127.3 KiB/414.1 KiB (1007.7 KiB/s) with 3 file(s) remaining\rCompleted 298.9 KiB/414.1 KiB (2.3 MiB/s) with 3 file(s) remaining   \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/curation_image.png\nCompleted 298.9 KiB/414.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 410.3 KiB/414.1 KiB (3.0 MiB/s) with 2 file(s) remaining\rupload: contents/Cui2008.xml to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/Cui2008.xml\nCompleted 410.3 KiB/414.1 KiB (3.0 MiB/s) with 1 file(s) remaining\rCompleted 414.1 KiB/414.1 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.0 KiB/8.0 KiB (118.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1846262268786a36358/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Cui2008.sedml\ncreating dataset /Cui2008.sedml/autogen_report_for_task1, shape: (22, 451), type: float64\ndataset created, uuid: d-52208f2d-d64636f3-c1e2-3ea655-db0ee4, chunk_size: (22, 451)\ncreating dataset /Cui2008.sedml/plot_1_task1, shape: (4, 451), type: float64\ndataset created, uuid: d-52208f2d-d64636f3-3703-8f562b-481cc4, chunk_size: (4, 451)\ncreating dataset /Cui2008.sedml/plot_2_task1, shape: (4, 451), type: float64\ndataset created, uuid: d-52208f2d-d64636f3-fb74-c164a3-8328b3, chunk_size: (4, 451)\ncreating attribute combineArchiveLocation in /Cui2008.sedml\ncreating attribute uri in /Cui2008.sedml\ncreating attribute _type in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute uri in /Cui2008.sedml/autogen_report_for_task1\ncreating attribute _type in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlId in /Cui2008.sedml/plot_1_task1\ncreating attribute sedmlName in /Cui2008.sedml/plot_1_task1\ncreating attribute uri in /Cui2008.sedml/plot_1_task1\ncreating attribute _type in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlId in /Cui2008.sedml/plot_2_task1\ncreating attribute sedmlName in /Cui2008.sedml/plot_2_task1\ncreating attribute uri in /Cui2008.sedml/plot_2_task1\ncreate_links: /\ngot link: Cui2008.sedml\ncreate_links: /Cui2008.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Cui2008.sedml/autogen_report_for_task1 to tgt: /Cui2008.sedml/autogen_report_for_task1, shape: (22, 451), type: float64\niterating over chunks for /Cui2008.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 22, 1), slice(0, 451, 1))\ndone with dataload for /Cui2008.sedml/autogen_report_for_task1\nwrite_dataset src: /Cui2008.sedml/plot_1_task1 to tgt: /Cui2008.sedml/plot_1_task1, shape: (4, 451), type: float64\niterating over chunks for /Cui2008.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 451, 1))\ndone with dataload for /Cui2008.sedml/plot_1_task1\nwrite_dataset src: /Cui2008.sedml/plot_2_task1 to tgt: /Cui2008.sedml/plot_2_task1, shape: (4, 451), type: float64\niterating over chunks for /Cui2008.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 451, 1))\ndone with dataload for /Cui2008.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f1846262268786a36358\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 the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve 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 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":7.134668,"sedDocuments":[{"location":"Cui2008.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  Cui2008.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 22 data sets\r\n    Plots (2):\r\n      plot_1_task1: 3 curves\r\n      plot_2_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Cui2008.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_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 \"Cui2008.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/tmpaj30j7z6/Cui2008.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['r3', 'r4', 'k_1', 'k2', 'k_2', 'Zn', 'k1a'] \r\n\r\nFast attribute ignored for reactions:\r\n['Formation_of_the_Zn4Zur_complex', 'Dissociation_of_Zn4Zur_complex', 'Formation_of_DNA_binding_complex', 'Disassociation_of_DNA_binding_complex', 'Formation_of_transcription_initiation_complex', 'Disassociation_of_transcription_initiation_complex'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"Formation_of_the_Zn4Zur_complex\" in default compartment\r\nInfo: single compartment model: locating \"Dissociation_of_Zn4Zur_complex\" in default compartment\r\nInfo: single compartment model: locating \"Formation_of_DNA_binding_complex\" in default compartment\r\nInfo: single compartment model: locating \"Disassociation_of_DNA_binding_complex\" in default compartment\r\nInfo: single compartment model: locating \"Formation_of_transcription_initiation_complex\" in default compartment\r\nInfo: single compartment model: locating \"Disassociation_of_transcription_initiation_complex\" in default compartment\r\nWriting file: /tmp/tmpn6ohz40z.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpaj30j7z6/Cui2008.xml\r\nout: /tmp/tmpn6ohz40z.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpn6ohz40z.psc loading ..... \r\nParsing file: /tmp/tmpn6ohz40z.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 451 points: 0.044051408767700195\r\n \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":6.866465,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":6.198292,"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":0.270165,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.140712,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"},{"id":"p2_curve_2_task1","status":"SUCCEEDED"},{"id":"p2_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.108759,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Py","status":"SUCCEEDED"},{"id":"autogen_task1_Py1","status":"SUCCEEDED"},{"id":"autogen_task1_Rw","status":"SUCCEEDED"},{"id":"autogen_task1_Dw","status":"SUCCEEDED"},{"id":"autogen_task1_Qw1","status":"SUCCEEDED"},{"id":"autogen_task1_Qw2","status":"SUCCEEDED"},{"id":"autogen_task1_Zn_2","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_r4","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_Zn","status":"SUCCEEDED"},{"id":"autogen_task1_k1a","status":"SUCCEEDED"},{"id":"autogen_task1_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_the_Zn4Zur_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Dissociation_of_Zn4Zur_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_DNA_binding_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Disassociation_of_DNA_binding_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_transcription_initiation_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Disassociation_of_transcription_initiation_complex","status":"SUCCEEDED"}]}]}]}