[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:128) - Initializing Python... []{}
 INFO (CLIPythonManager:153) - 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_54c0010d-4935-4f23-87ed-96e0b395b9cc10219777287202166588 []{}
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_03765275-fc43-419a-a7e9-802734507bfa16414556229207807408 []{}
 WARN (OmexHandler:144) - No SED-MLs are marked as master, so will run them all []{}
 WARN (OmexHandler:144) - No SED-MLs are marked as master, so will run them all []{}
 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: vonDassow2000_1x4.timecourse1.sedml []{}
 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  5 plot2D(s), and 0 plot3D(s)
 []{}
 INFO (SedmlJob:166) - Successful translation of SED-ML file : vonDassow2000_1x4.timecourse1.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
 WARN (XMLNodeReader:261) - The type of String 'annotation' on the element model (Model) is unknown! Some data might be lost. []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@10f7918f(id=null, name='PTC_T_0_0', species='PTC_T_0_0', structure='cell_0_0', sbmlName='PTC_T_0,0')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@64d4f7c7(id=null, name='EWG_T_0_0', species='EWG_T_0_0', structure='cell_0_0', sbmlName='EWG_T_0,0')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@984169e(id=null, name='PTC_T_0_2', species='PTC_T_0_2', structure='cell_0_2', sbmlName='PTC_T_0,2')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@43f1bb92(id=null, name='EWG_T_0_2', species='EWG_T_0_2', structure='cell_0_0', sbmlName='EWG_T_0,2')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@54e02f6a(id=null, name='PH_T_0_0', species='PH_T_0_0', structure='cell_0_0', sbmlName='PH_T_0,0')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@544e8149(id=null, name='PTC_T_0_3', species='PTC_T_0_3', structure='cell_0_3', sbmlName='PTC_T_0,3')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@1a96d94c(id=null, name='PH_T_0_3', species='PH_T_0_3', structure='cell_0_3', sbmlName='PH_T_0,3')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@6d6bbd35(id=null, name='PH_T_0_2', species='PH_T_0_2', structure='cell_0_2', sbmlName='PH_T_0,2')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@7fb66650(id=null, name='EWG_T_0_3', species='EWG_T_0_3', structure='cell_0_0', sbmlName='EWG_T_0,3')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@79a04e5f(id=null, name='PTC_T_0_1', species='PTC_T_0_1', structure='cell_0_1', sbmlName='PTC_T_0,1')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@66b59b7d(id=null, name='EWG_T_0_1', species='EWG_T_0_1', structure='cell_0_0', sbmlName='EWG_T_0,1')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
ERROR (SBMLImporter:1362) - unexpected assignment rule target 'SpeciesContext@53311681(id=null, name='PH_T_0_1', species='PH_T_0_1', structure='cell_0_1', sbmlName='PH_T_0,1')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1363) - need to create a VCLogger event []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R01_0_1 to distributed: linear factor was null, lumped reaction R01_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R01_0_2 to distributed: linear factor was null, lumped reaction R01_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R01_0_3 to distributed: linear factor was null, lumped reaction R01_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_1_0_0 to distributed: linear factor was null, lumped reaction R30a_1_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_1_0_0 to distributed: linear factor was null, lumped reaction R30b_1_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_1_0_0 to distributed: linear factor was null, lumped reaction R31_1_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_4_0_0 to distributed: linear factor was null, lumped reaction R30a_4_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_4_0_0 to distributed: linear factor was null, lumped reaction R30b_4_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_4_0_0 to distributed: linear factor was null, lumped reaction R31_4_0_0 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_1_0_1 to distributed: linear factor was null, lumped reaction R30a_1_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_1_0_1 to distributed: linear factor was null, lumped reaction R30b_1_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_1_0_1 to distributed: linear factor was null, lumped reaction R31_1_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_4_0_1 to distributed: linear factor was null, lumped reaction R30a_4_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_4_0_1 to distributed: linear factor was null, lumped reaction R30b_4_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_4_0_1 to distributed: linear factor was null, lumped reaction R31_4_0_1 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_1_0_2 to distributed: linear factor was null, lumped reaction R30a_1_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_1_0_2 to distributed: linear factor was null, lumped reaction R30b_1_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_1_0_2 to distributed: linear factor was null, lumped reaction R31_1_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_4_0_2 to distributed: linear factor was null, lumped reaction R30a_4_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_4_0_2 to distributed: linear factor was null, lumped reaction R30b_4_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_4_0_2 to distributed: linear factor was null, lumped reaction R31_4_0_2 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_1_0_3 to distributed: linear factor was null, lumped reaction R30a_1_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_1_0_3 to distributed: linear factor was null, lumped reaction R30b_1_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_1_0_3 to distributed: linear factor was null, lumped reaction R31_1_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30a_4_0_3 to distributed: linear factor was null, lumped reaction R30a_4_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30b_4_0_3 to distributed: linear factor was null, lumped reaction R30b_4_0_3 could not be transformed to distributed []{}
 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31_4_0_3 to distributed: linear factor was null, lumped reaction R31_4_0_3 could not be transformed to distributed []{}
 INFO (SimulationContext:3289) - mathMapping: message = transforming the Rate Rules... []{}
 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 INFO (SEDMLImporter:183) - Task (id='task1') is compatible, solver match found in ontology: 'KISAO:0000694' matched to CVODE []{}
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.solver.ode.CVodeSolverStandalone@4d5e136e []{}
 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:477) - Succesful execution: Model 'archive_vonDassow2000_1x4.timecourse1.sedml_model' Task 'task1'. []{}
 INFO (SolverHandler:489) - Running simulation task1_task1, 971 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_2_task1` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_3_task1` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_4_task1` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_5_task1` while CSV generation. []{}
 INFO (RunUtils:196) - Ignoring unsupported output `plot_6_task1` while CSV generation. []{}
 INFO (RunUtils:202) - Generating report `report_task1`. []{}
 INFO (RunUtils:381) - created csv file for report report_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/report_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_2_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_2_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/__plot__plot_2_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_3_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_3_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/__plot__plot_3_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_4_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_4_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/__plot__plot_4_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_5_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_5_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/__plot__plot_5_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__plot_6_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__plot_6_task1: /tmp/VCell_CLI_1939d9d55371618219224846650058/vonDassow2000_1x4.timecourse1.sedml/__plot__plot_6_task1.csv []{}
 INFO (SedmlJob:380) - Generating Plots...  []{}
 INFO (SedmlJob:391) - Generating HDF5 file...  []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_2_task1` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_3_task1` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_4_task1` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_5_task1` while CSV generation. []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_6_task1` 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 : vonDassow2000_1x4.timecourse1.sedml successfully completed []{}
 INFO (ExecutionJob:144) - Processing of SedML succeeded.
	> 1 model
	> 1 simulation
	> 1 task
	> 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_1939d9d55371618219224846650058 []{}
 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 (36s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 17.7 KiB/17.7 KiB (196.3 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67535b72707aa641045f00dd/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 9.1 KiB/9.1 KiB (88.2 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/67535b72707aa641045f00dd/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
  adding: outputs/log.yml (deflated 90%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/ (stored 0%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_5_task1.csv (deflated 57%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_3_task1.pdf (deflated 28%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_2_task1.csv (deflated 56%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_2_task1.pdf (deflated 26%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_4_task1.pdf (deflated 32%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/report_task1.csv (deflated 63%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_5_task1.pdf (deflated 31%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_4_task1.csv (deflated 73%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_6_task1.csv (deflated 54%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_6_task1.pdf (deflated 28%)
  adding: outputs/vonDassow2000_1x4.timecourse1.sedml/plot_3_task1.csv (deflated 54%)
  adding: outputs/reports.zip (stored 0%)
  adding: outputs/log.json (deflated 96%)
  adding: outputs/reports.h5 (deflated 35%)
