[0;36mThank you for using runBioSimulations![0m

[0;36m================================================ Loading Singularity ================================================[0m

[0;36m=================================================== Set up storage ==================================================[0m

[0;36m========================================== Downloading COMBINE/OMEX archive =========================================[0m
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[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================[0m
INFO:    Using cached SIF image
docker: Command recieved::<-i /root/archive.omex -o /root/outputs>
<-i>
Default case selected
VCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
 INFO (CLIStandalone:36) - Starting Vcell... []{}
 INFO (BiosimulationsCommand:94) - Beginning execution []{}
 INFO (CLIPythonManager:125) - Initializing Python... []{}
 INFO (CLIPythonManager:150) - Python initialization success! []{}
 INFO (ExecuteImpl:134) - Preparing output directory... []{}
 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}
 INFO (ExecutionJob:84) - Archive location: /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4f3574ff-7e38-44b1-ada6-5d037d2e275d12748670838337469022 []{}
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f3a784cd-3714-42c8-9a1a-14971e1632257480152067136415296 []{}
 INFO (SedmlJob:110) - Initializing SED-ML document... []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
 INFO (SedmlJob:125) - Processing SED-ML: Theinmozhi_2018.sedml []{}
 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 2 task(s), 1  report(s),  5 plot2D(s), and 0 plot3D(s)
 []{}
 INFO (SedmlJob:166) - Successful translation of SED-ML file : Theinmozhi_2018.sedml []{}
-----------------------------------------------------------------------------------------------------
 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}
 INFO (SedmlJob:186) - Creating Biomodel from pseudo SED-ML []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
 INFO (SedmlJob:261) - Building solvers and starting simulation of all tasks...  []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@5df778c3(id=null, name='SLP76t', species='SLP76t', structure='Cell', sbmlName='SLP76t')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@3c5dbdf8(id=null, name='ZAP70t', species='ZAP70t', structure='Cell', sbmlName='ZAP70t')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@2849434b(id=null, name='CD28t', species='CD28t', structure='Cell', sbmlName='CD28t')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@767a014e(id=null, name='LCKactive', species='LCKactive', structure='Cell', sbmlName='LCKactive')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@a66e580(id=null, name='LATt', species='LATt', structure='Cell', sbmlName='LATt')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@6edcad64(id=null, name='LCKinactive', species='LCKinactive', structure='Cell', sbmlName='LCKinactive')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@43e9089(id=null, name='PI3Kt', species='PI3Kt', structure='Cell', sbmlName='PI3Kt')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@895416d(id=null, name='CD3t', species='CD3t', structure='Cell', sbmlName='CD3t')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@4eba373c(id=null, name='LCKt', species='LCKt', structure='Cell', sbmlName='LCKt')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@2f5ac102(id=null, name='GADSt', species='GADSt', structure='Cell', sbmlName='GADSt')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@70228253(id=null, name='CPactive', species='CPactive', structure='Cell', sbmlName='CPactive')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
 INFO (SimulationContext:3289) - mathMapping: message = transforming the Rate Rules... []{}
ERROR (SEDMLImporter:187) - Task (id='task1)' is not compatible, no equivalent solver found in ontology for requested algorithm 'KISAO:0000694'; trying with deterministic default solver CombinedSundials []{}
ERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000571' not supported at this time, skipping. []{}
ERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000216' not supported at this time, skipping. []{}
ERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000415' not supported at this time, skipping. []{}
taskToSimulationMap: 1
taskToListOfSubTasksMap: 1
taskToVariableMap: 1
topTaskToBaseTask: 1
 INFO (SolverHandler:430) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@46de118b []{}
 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:477) - Succesful execution: Model 'archive_Theinmozhi_2018.sedml_model' Task 'task1'. []{}
 INFO (SolverHandler:489) - Running simulation task1_task1, 302 ms []{}
-----------------------------------------------------------------------------------------------------
 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}
 INFO (SedmlJob:302) - Generating outputs...  []{}
 INFO (SedmlJob:357) - Generating CSV file...  []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_6_task2` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_7_task2` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_8_task2` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_9_task2` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_10_task2` while CSV generation. []{}
 INFO (RunUtils:202) - Generating report `autogen_report_for_task2`. []{}
 INFO (RunUtils:381) - created csv file for report autogen_report_for_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/autogen_report_for_task2.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_6_task2`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_6_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/__plot__plot_6_task2.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_7_task2`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_7_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/__plot__plot_7_task2.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_8_task2`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_8_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/__plot__plot_8_task2.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_9_task2`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_9_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/__plot__plot_9_task2.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_10_task2`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_10_task2: /tmp/VCell_CLI_193b6021a4613324994923795465829/Theinmozhi_2018.sedml/__plot__plot_10_task2.csv []{}
 INFO (SedmlJob:380) - Generating Plots...  []{}
 INFO (SedmlJob:391) - Generating HDF5 file...  []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_6_task2` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_7_task2` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_8_task2` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_9_task2` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_10_task2` while CSV generation. []{}
 INFO (SedmlJob:343) - Archiving result files []{}
 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}
 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}
 INFO (SedmlJob:350) - SED-ML : Theinmozhi_2018.sedml successfully completed []{}
 INFO (ExecutionJob:144) - Processing of SedML succeeded.
	> 1 model
	> 1 simulation
	> 2 tasks
	> 6 outputs
		>> 1 report
		>> 5 2D plots
		>> 0 3D plots
	> Does not have Math Overrides
	> Does not have Parameter Scans []{}
 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_193b6021a4613324994923795465829 []{}
 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}
 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}
 INFO (ExecutionJob:174) - Omex archive.omex processing completed (15s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 11.4 KiB/11.4 KiB (152.2 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67599a0e9fa297efdca4d411/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 8.7 KiB/8.7 KiB (50.4 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/67599a0e9fa297efdca4d411/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
  adding: outputs/log.yml (deflated 88%)
  adding: outputs/reports.zip (stored 0%)
  adding: outputs/log.json (deflated 95%)
  adding: outputs/Theinmozhi_2018.sedml/ (stored 0%)
  adding: outputs/Theinmozhi_2018.sedml/plot_9_task2.pdf (deflated 32%)
  adding: outputs/Theinmozhi_2018.sedml/autogen_report_for_task2.csv (deflated 64%)
  adding: outputs/Theinmozhi_2018.sedml/plot_10_task2.csv (deflated 51%)
  adding: outputs/Theinmozhi_2018.sedml/plot_10_task2.pdf (deflated 32%)
  adding: outputs/Theinmozhi_2018.sedml/plot_6_task2.pdf (deflated 32%)
  adding: outputs/Theinmozhi_2018.sedml/plot_8_task2.csv (deflated 57%)
  adding: outputs/Theinmozhi_2018.sedml/plot_7_task2.csv (deflated 54%)
  adding: outputs/Theinmozhi_2018.sedml/plot_8_task2.pdf (deflated 30%)
  adding: outputs/Theinmozhi_2018.sedml/plot_6_task2.csv (deflated 53%)
  adding: outputs/Theinmozhi_2018.sedml/plot_7_task2.pdf (deflated 31%)
  adding: outputs/Theinmozhi_2018.sedml/plot_9_task2.csv (deflated 50%)
  adding: outputs/reports.h5 (deflated 55%)
