{"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    445      0 --:--:-- --:--:-- --:--:--   446\n\r100  108k  100  108k    0     0   252k      0 --:--:-- --:--:-- --:--:--  252k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n10:48:55 [main] WARN  cbit.vcell.resource.PropertyLoader - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory\nServerID=7.3.0.16, SoftwareVersion=unknown\nVCell CLI input archive /root/archive.omex\n-----------------------------------------------------------------------------------------------------\nTempPath Created: /tmp/vcell_temp_d64147b3-f4b1-49cf-a94e-6fca0fc6e29c6247410190066939355\nPython 3.8.10\nutilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils\ncliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils\ncliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py\nstatusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py\nFound 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)\n\nSuccessful translation of SED-ML file : biomodel_95682290.sedml\n-----------------------------------------------------------------------------------------------------\nname:  biomodel_95682290\nsedml_name:  biomodel_95682290\ncontent.location:  ./biomodel_95682290.sedml\ncontent_filename:  /root/outputs/temp/./biomodel_95682290.sedml\nStarting simulate all tasks... \nModel [id=ode, name=ode, language=urn:sedml:language:sbml, src=biomodel_95682290_ode.xml]\nThere are 0 changes.\nUniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Simulation0]\nTask [modelReference=ode, name=Simulation0, simulationReference=Simulation0, getId()=tsk_0_0]\nDataGenerator [math=org.jmathml.ASTRootNode@34f22f9d, name=time_tsk_0_0, getId()=time_tsk_0_0]\nDataGenerator [math=org.jmathml.ASTRootNode@3d1848cc, name=dataGen_tsk_0_0_PDE_cAMP, getId()=dataGen_tsk_0_0_PDE_cAMP]\nDataGenerator [math=org.jmathml.ASTRootNode@7dda48d9, name=dataGen_tsk_0_0_PDE_Cyto, getId()=dataGen_tsk_0_0_PDE_Cyto]\nDataGenerator [math=org.jmathml.ASTRootNode@6e4566f1, name=dataGen_tsk_0_0_cAMP_best, getId()=dataGen_tsk_0_0_cAMP_best]\nPlot2D [listOfCurves=[Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_cAMP, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_cAMP, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_cAMP], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_Cyto, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_Cyto, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_Cyto], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_cAMP_best, logX=false, logY=false, name=dataGen_tsk_0_0_cAMP_best, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_cAMP_best]], name=ode_Simulation0_plot]\norg.jlibsedml.Report@958bc87d\norg.jlibsedml.Report@5ce30dfd\nTask (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE\nnew symbol is uM,   old symbol is umol.l-1\nSBML Import: no assignment rules.\nSBML Import: no assignment rules.\nSuccesful model import: SBML file /tmp/temp3631924664232323065.xml\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:49:03 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n/root/outputs/biomodel_95682290.sedml\nfalse\ncbit.vcell.solver.ode.CVodeSolverStandalone@59942b48\nFinished: SOLVER_FINISHED:completed\nSuccesful execution: Model 'archive__ode' Task 'Simulation0'.\nRunning simulation tsk_0_0_Simulation0, 350 ms\n-----------------------------------------------------------------------------------------------------\nRan 1 simulations for 1 biomodels.\nIgnoring unsupported output `plot2d_Simulation0` while CSV generation.\nGenerating report `report_Simulation0`.\nGenerating report `__plot__plot2d_Simulation0`.\nIgnoring unsupported output `plot2d_Simulation0` while generating idNamePlotsMap.\n{'report_Simulation0': 'ode_Simulation0_plot', '__plot__plot2d_Simulation0': 'ode_Simulation0_plot', 'plot2d_Simulation0': 'ode_Simulation0_plot'}\n__plot__plot2d_Simulation0\nreport   :  /root/outputs/./biomodel_95682290.sedml/report_Simulation0.csv\nreport_Simulation0\nHDF conversion successful\nArchiving resultant PDF files to `plots.zip`.\nArchiving resultant CSV files to `reports.zip`.\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 6.2 KiB/6.2 KiB (34.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/rawLog.txt\nCompleted 1.5 KiB/1.5 KiB (14.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/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/biomodel_95682290.sedml/ (stored 0%)\n  adding: outputs/biomodel_95682290.sedml/idNamePlotsMap.txt (deflated 67%)\n  adding: outputs/biomodel_95682290.sedml/plot2d_Simulation0.pdf (deflated 30%)\n  adding: outputs/biomodel_95682290.sedml/report_Simulation0.csv (deflated 56%)\n  adding: outputs/biomodel_95682290.sedml/plot2d_Simulation0.csv (deflated 56%)\n  adding: outputs/reports.zip (stored 0%)\n  adding: outputs/log.json (deflated 84%)\n  adding: outputs/fullSuccessLog.txt (stored 0%)\n  adding: outputs/reports.h5 (deflated 32%)\n  adding: outputs/detailedResultLog.txt (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 73.4 KiB/73.4 KiB (336.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/reports.h5\nCompleted 181.3 KiB/413.0 KiB (1.1 MiB/s) with 13 file(s) remaining\rCompleted 184.3 KiB/413.0 KiB (1.1 MiB/s) with 13 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/log.json\nCompleted 184.3 KiB/413.0 KiB (1.1 MiB/s) with 12 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/output.zip\nCompleted 184.3 KiB/413.0 KiB (1.1 MiB/s) with 11 file(s) remaining\rCompleted 184.4 KiB/413.0 KiB (1.1 MiB/s) with 11 file(s) remaining\rupload: outputs/biomodel_95682290.sedml/idNamePlotsMap.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/biomodel_95682290.sedml/idNamePlotsMap.txt\nCompleted 184.4 KiB/413.0 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 250.4 KiB/413.0 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: outputs/biomodel_95682290.sedml/plot2d_Simulation0.csv to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/biomodel_95682290.sedml/plot2d_Simulation0.csv\nCompleted 250.4 KiB/413.0 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 261.5 KiB/413.0 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/plots.zip\nCompleted 261.5 KiB/413.0 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 261.9 KiB/413.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: ./stdOut.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/stdOut.txt\nCompleted 261.9 KiB/413.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 265.9 KiB/413.0 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: ./temp16548077358469308861804289383.tmp to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/temp16548077358469308861804289383.tmp\nCompleted 265.9 KiB/413.0 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 323.7 KiB/413.0 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/reports.zip\nCompleted 323.7 KiB/413.0 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 331.3 KiB/413.0 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/rawLog.txt\nCompleted 331.3 KiB/413.0 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 331.4 KiB/413.0 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: outputs/detailedResultLog.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/detailedResultLog.txt\nCompleted 331.4 KiB/413.0 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/biomodel_95682290.sedml/plot2d_Simulation0.pdf to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/biomodel_95682290.sedml/plot2d_Simulation0.pdf\nCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/fullSuccessLog.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/fullSuccessLog.txt\nCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 413.0 KiB/413.0 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/biomodel_95682290.sedml/report_Simulation0.csv to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/outputs/biomodel_95682290.sedml/report_Simulation0.csv\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/diagram.png    \n  inflating: contents/biomodel_95682290_ode.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/biomodel_95682290.sedml  \n  inflating: contents/biomodel_95682290.vcml  \n  inflating: contents/manifest.xml   \nCompleted 256.0 KiB/293.2 KiB (5.7 MiB/s) with 6 file(s) remaining\rCompleted 266.5 KiB/293.2 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/biomodel_95682290.vcml to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/biomodel_95682290.vcml\nCompleted 266.5 KiB/293.2 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 276.7 KiB/293.2 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/biomodel_95682290_ode.xml to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/biomodel_95682290_ode.xml\nCompleted 276.7 KiB/293.2 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 281.5 KiB/293.2 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/biomodel_95682290.sedml to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/biomodel_95682290.sedml\nCompleted 281.5 KiB/293.2 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 282.2 KiB/293.2 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/manifest.xml\nCompleted 282.2 KiB/293.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 289.2 KiB/293.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/diagram.png to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/diagram.png\nCompleted 289.2 KiB/293.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 293.2 KiB/293.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 13.1 KiB/13.1 KiB (108.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a216644ffe186f420c45ed/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /biomodel_95682290.sedml\ncreating dataset /biomodel_95682290.sedml/plot2d_Simulation0, shape: (4, 1001), type: float64\ndataset created, uuid: d-47972f85-460f8f0c-4571-8138c8-03b417, chunk_size: (4, 1001)\ncreating dataset /biomodel_95682290.sedml/report_Simulation0, shape: (4, 1001), type: float64\ndataset created, uuid: d-47972f85-460f8f0c-2b5b-79c3ac-c00ca7, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /biomodel_95682290.sedml\ncreating attribute uri in /biomodel_95682290.sedml\ncreating attribute _type in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlId in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute sedmlName in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute uri in /biomodel_95682290.sedml/plot2d_Simulation0\ncreating attribute _type in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlId in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute sedmlName in /biomodel_95682290.sedml/report_Simulation0\ncreating attribute uri in /biomodel_95682290.sedml/report_Simulation0\ncreate_links: /\ngot link: biomodel_95682290.sedml\ncreate_links: /biomodel_95682290.sedml\ngot link: plot2d_Simulation0\ngot link: report_Simulation0\nwrite_dataset src: /biomodel_95682290.sedml/plot2d_Simulation0 to tgt: /biomodel_95682290.sedml/plot2d_Simulation0, shape: (4, 1001), type: float64\niterating over chunks for /biomodel_95682290.sedml/plot2d_Simulation0\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95682290.sedml/plot2d_Simulation0\nwrite_dataset src: /biomodel_95682290.sedml/report_Simulation0 to tgt: /biomodel_95682290.sedml/report_Simulation0, shape: (4, 1001), type: float64\niterating over chunks for /biomodel_95682290.sedml/report_Simulation0\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95682290.sedml/report_Simulation0\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/62a216644ffe186f420c45ed\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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":19,"sedDocuments":[{"location":"biomodel_95682290.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ","duration":null,"tasks":[{"id":"tsk_0_0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing simulation... done. Starting simulation... done. ","duration":1,"algorithm":"KISAO_0000019","simulatorDetails":null}],"outputs":[{"id":"plot2d_Simulation0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_cAMP","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_Cyto","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_cAMP_best","status":"SUCCEEDED"}]},{"id":"report_Simulation0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"__data_set__plot2d_Simulation0time_tsk_0_0","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_PDE_cAMP","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_PDE_Cyto","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_cAMP_best","status":"SUCCEEDED"}]}]}]}