{"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    401      0 --:--:-- --:--:-- --:--:--   402\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  204k  100  204k    0     0   428k      0 --:--:-- --:--:-- --:--:-- 2729k\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 3.0 KiB/3.0 KiB (45.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/rawLog.txt\nCompleted 5.6 KiB/5.6 KiB (49.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 70%)\n  adding: outputs/BIOMD0000000044_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000044_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 65%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 126.9 KiB/126.9 KiB (963.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/outputs/reports.h5\nCompleted 22.6 KiB/156.1 KiB (293.6 KiB/s) with 5 file(s) remaining\rupload: ./_pystmptmptdkioj5r_parsetab.py to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/_pystmptmptdkioj5r_parsetab.py\nCompleted 22.6 KiB/156.1 KiB (293.6 KiB/s) with 4 file(s) remaining\rCompleted 31.1 KiB/156.1 KiB (247.7 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000044_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/outputs/BIOMD0000000044_url.sedml/autogen_plot_for_task1.pdf\nCompleted 31.1 KiB/156.1 KiB (247.7 KiB/s) with 3 file(s) remaining\rCompleted 36.8 KiB/156.1 KiB (266.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/outputs/plots.zip\nCompleted 36.8 KiB/156.1 KiB (266.7 KiB/s) with 2 file(s) remaining\rCompleted 152.1 KiB/156.1 KiB (983.2 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/output.zip\nCompleted 152.1 KiB/156.1 KiB (983.2 KiB/s) with 1 file(s) remaining\rCompleted 156.1 KiB/156.1 KiB (781.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000044-biopax2.owl  \n  inflating: contents/BIOMD0000000044-biopax3.owl  \n  inflating: contents/BIOMD0000000044-matlab.m  \n  inflating: contents/BIOMD0000000044-octave.m  \n  inflating: contents/BIOMD0000000044.m  \n  inflating: contents/BIOMD0000000044.ode  \n  inflating: contents/BIOMD0000000044.pdf  \n  inflating: contents/BIOMD0000000044.png  \n  inflating: contents/BIOMD0000000044.sci  \n  inflating: contents/BIOMD0000000044.svg  \n  inflating: contents/BIOMD0000000044.vcml  \n  inflating: contents/BIOMD0000000044_url.sedml  \n  inflating: contents/BIOMD0000000044_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 15.4 KiB/~358.6 KiB (166.3 KiB/s) with ~13 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000044-biopax2.owl to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044-biopax2.owl\nCompleted 15.4 KiB/~358.6 KiB (166.3 KiB/s) with ~12 file(s) remaining (calculating...)\rCompleted 20.5 KiB/378.1 KiB (145.6 KiB/s) with 16 file(s) remaining                   \rupload: contents/BIOMD0000000044-octave.m to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044-octave.m\nCompleted 20.5 KiB/378.1 KiB (145.6 KiB/s) with 15 file(s) remaining\rCompleted 25.6 KiB/378.1 KiB (175.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000044-matlab.m to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044-matlab.m\nCompleted 25.6 KiB/378.1 KiB (175.6 KiB/s) with 14 file(s) remaining\rCompleted 46.2 KiB/378.1 KiB (307.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000044-biopax3.owl to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044-biopax3.owl\nCompleted 46.2 KiB/378.1 KiB (307.7 KiB/s) with 13 file(s) remaining\rCompleted 72.1 KiB/378.1 KiB (442.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000044_url.xml to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044_url.xml\nCompleted 72.1 KiB/378.1 KiB (442.1 KiB/s) with 12 file(s) remaining\rCompleted 77.3 KiB/378.1 KiB (387.4 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/metadata.rdf\nCompleted 77.3 KiB/378.1 KiB (387.4 KiB/s) with 11 file(s) remaining\rCompleted 80.5 KiB/378.1 KiB (395.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000044.sci to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.sci\nCompleted 80.5 KiB/378.1 KiB (395.4 KiB/s) with 10 file(s) remaining\rCompleted 82.4 KiB/378.1 KiB (394.6 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/manifest.xml\nCompleted 82.4 KiB/378.1 KiB (394.6 KiB/s) with 9 file(s) remaining\rCompleted 115.4 KiB/378.1 KiB (539.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000044.vcml to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.vcml\nCompleted 115.4 KiB/378.1 KiB (539.2 KiB/s) with 8 file(s) remaining\rCompleted 155.4 KiB/378.1 KiB (699.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000044.png to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.png\nCompleted 155.4 KiB/378.1 KiB (699.3 KiB/s) with 7 file(s) remaining\rCompleted 333.8 KiB/378.1 KiB (1.4 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000044.pdf to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.pdf\nCompleted 333.8 KiB/378.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 348.1 KiB/378.1 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000044.svg to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.svg\nCompleted 348.1 KiB/378.1 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 360.1 KiB/378.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/curation_image.png\nCompleted 360.1 KiB/378.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 360.4 KiB/378.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 370.3 KiB/378.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000044_url.sedml to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044_url.sedml\nCompleted 370.3 KiB/378.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/curation_notes.txt\nCompleted 370.3 KiB/378.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 373.0 KiB/378.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000044.ode to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.ode\nCompleted 373.0 KiB/378.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 378.1 KiB/378.1 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000044.m to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/contents/BIOMD0000000044.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.9 KiB/10.9 KiB (97.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488b9d96262268786a25f23/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000044_url.sedml\ncreating dataset /BIOMD0000000044_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-d2c52106-5ea5c96c-a157-ec4909-f46815, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000044_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-d2c52106-5ea5c96c-db82-419971-bb3fc7, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000044_url.sedml\ncreating attribute uri in /BIOMD0000000044_url.sedml\ncreating attribute _type in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000044_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000044_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000044_url.sedml\ncreate_links: /BIOMD0000000044_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000044_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000044_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000044_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000044_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000044_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000044_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000044_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000044_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488b9d96262268786a25f23\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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.006334,"sedDocuments":[{"location":"BIOMD0000000044_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  BIOMD0000000044_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000044_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: multiple compartments defined but reaction vin is not located in any of them.\r\nInfo: multiple compartments defined but reaction v2 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v3 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v4 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v5 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v6 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v7 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v8 is not located in any of them.\r\nWriting file: /tmp/tmptdkioj5r.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpi_c6pjfh/BIOMD0000000044_url.xml\r\nout: /tmp/tmptdkioj5r.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmptdkioj5r.psc loading ..... \r\nParsing file: /tmp/tmptdkioj5r.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 1001 points: 0.39223265647888184\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":1.547743,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.590074,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.26199,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EC","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_intravesicular","status":"SUCCEEDED"},{"id":"autogen_task1_vin","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.558768,"curves":[{"id":"autogen_curve_task1_EC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"}]}]}]}