Submit VCell 7.7.0.19

[CodeByDrescher]

Simulation tool

---

id: vcell
version: 7.7.0.19
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.7.0.19/biosimulators.json
specificationsPatch:
version: 7.7.0.19
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.7.0.19
digest: "sha256:4c0ba1c711ec5f8917135a762e59feed2397abe9b3aa107cc84ac0dfe4fecc5d"
validateImage: true
commitSimulator: true

Support for BioSimulators' conventions

• The simulation tool is provided as a Docker image
• The ENTRYPOINT of the image is a BioSimulators-compliant command-line interface
• This command-line interface supports the COMBINE/OMEX archive format
• This command-line interface supports the Simulation Experiment Description Markup Language (SED-ML) format
• This command-line interface supports the Hierarchical Data Format (HDF5)
• The capabilities of the tool are described using BioSimulators' format
• The modeling frameworks supported by the tool are described using Systems Biology Ontology (SBO) terms
• The algorithms supported by the tool are described using Kinetic Simulation Algorithm Ontology (KiSAO) ontology terms
• The model formats supported by the tool are described using EMBRACE Data and Methods (EDAM) ontology terms
• The licenses supported by the tool are described using Software Package Data Exchange (SPDX) identifiers
• The source code for the simulation tool is publicly available
• The simulation tool is available through a software repository such as CRAN or PyPI
• The simulation tool is registered with bio.tools
• The Docker image provides Open Containers Initiative-compliant metadata
• The Docker image provides BioContainers-compliant metadata
• The Docker image is registered with BioContainers

[biosimulators-daemon]

Thank you @CodeByDrescher for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 74 test cases

• Passed 37 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • docker_image.SingularityImageExecutesSimulationsSuccessfully
  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

• Failed 2 test cases:

  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Skipped 35 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
  • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms

[biosimulators-daemon]

Failures

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (4.3 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Exception:

Data set data_set_time of report simulation.sedml/report does not have expected value at (0,): 399.0 != 400

Data set data_set_time of report simulation.sedml/report does not have expected value at (1,): 400.0 != 401

Data set data_set_time of report simulation.sedml/report does not have expected value at (2,): 401.0 != 402

Data set data_set_time of report simulation.sedml/report does not have expected value at (600,): 999.0 != 1000

Log:

docker: Command recieved::<-i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Elowitz-Nature-2000-Repressilator.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: simulation.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: simulation.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 2 outputs

		> 1 Report

		> 1 2D Plot

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction1 to distributed: linear factor was null, lumped reaction Reaction1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction2 to distributed: linear factor was null, lumped reaction Reaction2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction3 to distributed: linear factor was null, lumped reaction Reaction3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction4 to distributed: linear factor was null, lumped reaction Reaction4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction5 to distributed: linear factor was null, lumped reaction Reaction5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction6 to distributed: linear factor was null, lumped reaction Reaction6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction7 to distributed: linear factor was null, lumped reaction Reaction7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction8 to distributed: linear factor was null, lumped reaction Reaction8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction9 to distributed: linear factor was null, lumped reaction Reaction9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction10 to distributed: linear factor was null, lumped reaction Reaction10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction11 to distributed: linear factor was null, lumped reaction Reaction11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction12 to distributed: linear factor was null, lumped reaction Reaction12 could not be transformed to distributed []{}

 INFO (SEDMLImporter:192) - Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_467111276_0_0 (task)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.125s): Model 'Elowitz-Nature-2000-Repressilator_simulation.sedml_model' Task 'task' (task_task). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> task::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : simulation.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (simulation.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426f114b769457839302633041 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Elowitz-Nature-2000-Repressilator.omex` processing completed (2.301s) []{}

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (3.6 s)

Test that a simulator supports time courses with non-zero output start times

Exception:

Simulator did not produce the expected time course:

  
  Not equal to tolerance rtol=0.0001, atol=0
  
  Mismatched elements: 6 / 6 (100%)
  Max absolute difference: 0.2
  Max relative difference: 0.2
   x: array([0.8, 1. , 1.2, 1.4, 1.6, 1.8])
   y: array([1. , 1.2, 1.4, 1.6, 1.8, 2. ])

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 1 output

		> 1 Report

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_1620505269_0_0 (BIOMD0000000912_task)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.081s): Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010' (Caravagna2010). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> Caravagna2010 (BIOMD0000000912_task)::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (BIOMD0000000912_sim.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426e730d89639424021362936 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (1.494s) []{}

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (3.8 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  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:40) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:50) - ARCHIVE file not specified, try --help for usage []{}
  

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  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:40) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit
  

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  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:40) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit
  

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.3 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
  BIOMD0000000912_sim.sedml/Figure_1_bottom_left

Plots were not produced:
  BIOMD0000000912_sim.sedml/Figure_1_bottom_left

Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure 1 bottom, left

Log:

docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 2 outputs

		> 1 Report

		> 1 2D Plot

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_1315511506_0_0 (BIOMD0000000912_task)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.141s): Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010' (Caravagna2010). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> Caravagna2010 (BIOMD0000000912_task)::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (BIOMD0000000912_sim.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426ece483634810110197411967 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` processing completed (2.231s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (6.5 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000086

Warnings:

Unexpected reports were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Plots were not produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Extra plots were produced:
  simulation_1.sedml/Figure 3a
  simulation_1.sedml/Figure 3b
  simulation_1.sedml/Figure 3c
  simulation_1.sedml/Figure 3d

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: simulation_1.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: simulation_1.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 5 outputs

		> 1 Report

		> 4 2D Plots

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{}

 INFO (SEDMLImporter:192) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_794562589_0_0 (task_1)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.686s): Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1' (simulation 1). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> simulation 1 (task_1)::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : simulation_1.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (simulation_1.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426edf4379521505015289136 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` processing completed (4.266s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (6.2 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Plots were not produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Extra plots were produced:
  simulation_1.sedml/Figure 3a
  simulation_1.sedml/Figure 3b
  simulation_1.sedml/Figure 3c
  simulation_1.sedml/Figure 3d

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: simulation_1.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: simulation_1.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 5 outputs

		> 1 Report

		> 4 2D Plots

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{}

 INFO (SEDMLImporter:192) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_355753454_0_0 (task_1)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.157s): Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1' (simulation 1). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> simulation 1 (task_1)::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : simulation_1.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (simulation_1.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426ef90b3617773193048188940 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` processing completed (3.935s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (4.3 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
  simulation.sedml/Figure_1c

Plots were not produced:
  simulation.sedml/Figure_1c

Extra plots were produced:
  simulation.sedml/Figure 1c

Log:

docker: Command recieved::<-i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Elowitz-Nature-2000-Repressilator.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: simulation.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: simulation.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 2 outputs

		> 1 Report

		> 1 2D Plot

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction1 to distributed: linear factor was null, lumped reaction Reaction1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction2 to distributed: linear factor was null, lumped reaction Reaction2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction3 to distributed: linear factor was null, lumped reaction Reaction3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction4 to distributed: linear factor was null, lumped reaction Reaction4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction5 to distributed: linear factor was null, lumped reaction Reaction5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction6 to distributed: linear factor was null, lumped reaction Reaction6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction7 to distributed: linear factor was null, lumped reaction Reaction7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction8 to distributed: linear factor was null, lumped reaction Reaction8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction9 to distributed: linear factor was null, lumped reaction Reaction9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction10 to distributed: linear factor was null, lumped reaction Reaction10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction11 to distributed: linear factor was null, lumped reaction Reaction11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction Reaction12 to distributed: linear factor was null, lumped reaction Reaction12 could not be transformed to distributed []{}

 INFO (SEDMLImporter:192) - Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_467111276_0_0 (task)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.125s): Model 'Elowitz-Nature-2000-Repressilator_simulation.sedml_model' Task 'task' (task_task). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> task::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : simulation.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (simulation.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426f114b769457839302633041 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Elowitz-Nature-2000-Repressilator.omex` processing completed (2.301s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (6.2 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3b
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3c
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3d
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3e
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3f
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3g
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3h

Plots were not produced:
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3b
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3c
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3d
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3e
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3f
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3g
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3h

Extra plots were produced:
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3b
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3c
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3d
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3e
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3f
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3g
  Parmar2017_Deficient_Rich_tracer.sedml/Figure 3h

Log:

docker: Command recieved::<-i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: Parmar2017_Deficient_Rich_tracer.sedml []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: Parmar2017_Deficient_Rich_tracer.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 8 outputs

		> 1 Report

		> 7 2D Plots

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 INFO (SBMLImporter:966) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (___TIME_SYMBOL___ >= 35.0) []{}

 INFO (SEDMLImporter:192) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_2020644743_0_0 (task_1)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.194s): Model 'Parmar-BMC-Syst-Biol-2017-iron-distribution_Parmar2017_Deficient_Rich_tracer.sedml_model' Task 'task_1' (task_1_task_1). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 1 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> task_1::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : Parmar2017_Deficient_Rich_tracer.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (Parmar2017_Deficient_Rich_tracer.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426f226116901816778321335176 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` processing completed (4.027s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (12.6 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019
• Format: format_2585
  Algorithm: KISAO_0000027

Warnings:

Unexpected reports were produced:
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det
  simulation.sedml/plot2d_low_delta_R_stoch

Plots were not produced:
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det
  simulation.sedml/plot2d_low_delta_R_stoch

Extra plots were produced:
  simulation.sedml/ODE deterministicplots
  simulation.sedml/ODE stochasticplots

Log:

docker: Command recieved::<-i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Vilar-PNAS-2002-minimal-circardian-clock.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: simulation.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: simulation.sedml.

	> 4 models

	> 5 simulations

		> 5 Uniform Time Course simulations

	> 5 tasks

	> 10 outputs

		> 5 Reports

		> 5 2D Plots

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

 INFO (SEDMLImporter:192) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

 INFO (SEDMLImporter:192) - Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler []{}

 INFO (SEDMLImporter:192) - Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson []{}

 INFO (SEDMLImporter:192) - Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_287946819_0_0 (tsk_0_0)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.107s): Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_0' (tsk_0_0). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_388776518_0_0 (tsk_0_3)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (5.297s): Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_3' (tsk_0_3). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_1644404658_0_0 (tsk_1_0)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.21s): Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_0' (tsk_1_0). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_1655206893_0_0 (tsk_1_1)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.191s): Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic_0' Task 'tsk_1_1' (tsk_1_1). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_698263778_0_0 (tsk_0_1)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.057s): Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic_0' Task 'tsk_0_1' (tsk_0_1). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 5 simulation jobs for 4 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> tsk_0_0 (tsk_0_0)::SUCCEEDED

	> tsk_0_3 (tsk_0_3)::SUCCEEDED

	> tsk_1_0 (tsk_1_0)::SUCCEEDED

	> tsk_1_1 (tsk_1_1)::SUCCEEDED

	> tsk_0_1 (tsk_0_1)::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:356) - Generating Plots...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : simulation.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (simulation.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426f66cc2097089169830357344 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `Vilar-PNAS-2002-minimal-circardian-clock.omex` processing completed (10.09s) []{}

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (5.5 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
  simulation.sedml/Figure_2ab
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Plots were not produced:
  simulation.sedml/Figure_2ab
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Extra plots were produced:
  simulation.sedml/Figure 2ab
  simulation.sedml/ODE deterministicplots

Log:

docker: Command recieved::<-i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML docu ...

[biosimulators-daemon]

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_3972
  Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_3972
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_3240
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_3240
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9004
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9004
  Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9012
  Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585
  Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9001
  Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9010
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (9.2 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.19' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 1 output

		> 1 Report

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:327) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

ERROR (ExecutionJob:131) - SedML (@BIOMD0000000912_sim.sedml) processing failed: []{}

org.vcell.cli.exceptions.ExecutionException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:243) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (1.852s) []{}

ERROR (ExecutionJob:175) -  All sedml documents in this archive failed to execute []{}

ERROR (BiosimulationsCommand:105) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 1 output

		> 1 Report

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:327) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

ERROR (ExecutionJob:131) - SedML (@BIOMD0000000912_sim.sedml) processing failed: []{}

org.vcell.cli.exceptions.ExecutionException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:243) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (2.189s) []{}

ERROR (ExecutionJob:175) -  All sedml documents in this archive failed to execute []{}

ERROR (BiosimulationsCommand:105) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

sedml.SimulatorSupportsDataSetsWithDifferentShapes (3.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

Data set `__single_var_output_el__1` does not have the expected shape

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 2 simulations

		> 2 Uniform Time Course simulations

	> 2 tasks

	> 1 output

		> 1 Report

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_1939478487_0_0 (BIOMD0000000912_task)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.086s): Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010' (Caravagna2010). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:356) - Initializing simulation job SimID_201701192_0_0 (BIOMD0000000912_task__copy_2)... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:388) - Beginning Simulation... []{}

 INFO (SolverHandler:448) - Successful execution (0.031s): Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2' (BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2). []{}

 INFO (SolverHandler:518) - Processing non-spatial results of execution... []{}

-  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  --  -

 INFO (SolverHandler:556) - Ran 2 simulation jobs for 1 biomodels. []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:231) - Summary of Task Results

	> Caravagna2010 (BIOMD0000000912_task)::SUCCEEDED

	> BIOMD0000000912_task__copy_2::SUCCEEDED

 []{}

 INFO (SedmlJob:258) - Generating outputs...  []{}

 INFO (SedmlJob:341) - Generating CSV file...  []{}

 INFO (SedmlJob:374) - Indexing HDF5 data...  []{}

 INFO (SedmlJob:334) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:149) - Processing of SedML (BIOMD0000000912_sim.sedml) succeeded. []{}

 INFO (BiosimulationsHdf5Writer:40) - Creating HDF5 file `reports.h5` in /tmp/VCell_CLI_195426d187014004400139033672651 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:110) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (1.522s) []{}

sedml.SimulatorSupportsModelAttributeChanges (8.5 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.19' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 1 output

		> 1 Report

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:327) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:866) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:160) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:865) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:160) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

ERROR (ExecutionJob:131) - SedML (@BIOMD0000000912_sim.sedml) processing failed: []{}

org.vcell.cli.exceptions.ExecutionException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!

Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:243) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:866) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:160) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:865) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:160) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (1.357s) []{}

ERROR (ExecutionJob:175) -  All sedml documents in this archive failed to execute []{}

ERROR (BiosimulationsCommand:105) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: BIOMD0000000912 - IllegalArgumentException occurred: Must be of type int!

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. Errors reported: IllegalArgumentException occurred: Must be of type int!



 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 1 task

	> 1 output

		> 1 Report

	> Has Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:327) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

ERROR (ExecutionJob:131) - SedML (@BIOMD0000000912_sim.sedml) processing failed: []{}

org.vcell.cli.exceptions.ExecutionException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:243) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:919) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:324) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (ExecutionJob:165) - Omex `archive.omex` processing completed (2.701s) []{}

ERROR (ExecutionJob:175) -  All sedml documents in this archive failed to execute []{}

ERROR (BiosimulationsCommand:105) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

sedml.SimulatorSupportsRepeatedTasksWithChanges (11.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.19' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

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:40) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:99) - Beginning execution []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:116) - Initializing and Pre-Processing SedML document: BIOMD0000000912_sim.sedml []{}

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SedmlJob:173) - Successfully loaded and translated SED-ML file: BIOMD0000000912_sim.sedml.

	> 1 model

	> 1 simulation

		> 1 Uniform Time Course simulation

	> 2 tasks

	> 2 outputs

		> 2 Reports

	> Does not have Math Overrides

	> Has Parameter Scans []{}

 INFO (SedmlJob:215) - Building solvers and starting simulation of all tasks...  []{}

-----------------------------------------------------------------------------------------------------

 WARN (SchematronValidator:119) - Unsupported sedml version `L1V3` detected, validating as L1V2 []{}

 INFO (SEDMLImporter:192) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:327) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:379) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:325) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:47) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.createOverrides(SEDMLImporter.java:485) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.addRepeatedTasks(SEDMLImporter.java:805) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 20 more

ERROR (ExecutionJob:131) - SedML (@BIOMD0000000912_sim.sedml) processing failed: []{}

org.vcell.cli.exceptions.ExecutionException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:243) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:200) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeSedmlDocument(ExecutionJob.java:146) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:143) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:161) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.executeVCellBiosimulationsMode(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:64) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.commands.execution.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3 ...

[biosimulators-daemon]

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/13544754862). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/13544754862).