Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_VCell/921a4ddee847d109014b335f1896ed86f108b176/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>
validateImage: true
commitSimulator: true

Thank you @biosimulators-daemon 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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 67 test cases

Passed 22 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
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
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 6 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
docker_image.SingularityImageExecutesSimulationsSuccessfully
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

Skipped 39 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
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:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
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
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (12.7 s)
Test that SED documents in nested directories can be executed
Exception:
Simulator did not generate the following expected reports
  - `subdir/BIOMD0000000912_sim.sedml/report`

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 8:59:27 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_03689fa1-a754-496c-be00-ab3cc45e9a072299912556852962745

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp574364750218391927.xml

/tmp/out/subdir/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4e406694

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (20.2 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths
Exception:
Simulator did not generate the following expected reports
  - `subdir/BIOMD0000000912_sim.sedml/report`
  - `subdir__copy/BIOMD0000000912_sim.sedml/report`

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 8:59:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3b294fc9-97c5-4ae0-aef5-0c8b4384e87a4984895643144726098

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp8431889336959672628.xml

/tmp/out/subdir/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2b50150

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp3582556060374100709.xml

/tmp/out/subdir__copy/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7af1cd63

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

docker_image.SingularityImageExecutesSimulationsSuccessfully (15.5 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives
Exception:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (65.9 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Exception:
No reports were generated

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

Jun 24, 2021 9:08:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_535c56e8-ce6e-4542-8c1c-360e3426d5793590871764509728877

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6  report(s),  6 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp1051364932104824523.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp3132317495985170646.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp6499359265642292712.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp4841090033505093123.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@60cb1ed6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6b357eb6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.

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

cbit.vcell.solver.stoch.GibsonSolver@704067c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@78a8978a

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (46.2 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Exception:
No reports were generated

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex

Jun 24, 2021 9:07:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_a5d2a7bd-1c50-4629-ae36-b57ea723a305854981195349304287

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4  report(s),  5 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp1097096431627518935.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp134148435334896847.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5d0b0cb9

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@13e5d243

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.

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

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (27.5 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Exception:
No reports were generated

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex

Jun 24, 2021 9:07:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6c5977c9-e2f0-4c5f-8e99-d31d585940f6323766587966945789

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s),  2 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp4685888074448782656.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp828585248270185401.xml

cbit.vcell.solver.stoch.GibsonSolver@7573e12f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@1b005a0b

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 189, in exec_sed_doc

    rel_path=os.path.join(content.location, report.id).split("./")[1]

IndexError: list index out of range

HDF conversion failed

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (1.7 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'

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:

docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.6 s)
Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
  org.opencontainers.image.created
  org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (15.9 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

Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure_1

Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

Jun 24, 2021 9:05:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_f3509607-0c65-4d9b-ba67-00e39e9044b94366230651058973455

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp181165330232370847.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4c5204af

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.

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

Ignoring unsupported output `Figure_1` while CSV generation.

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

BIOMD0000000912_sim.sedml/Figure_1

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (29.5 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.sedml/Figure_3a
  simulation.sedml/Figure_3b
  simulation.sedml/Figure_3c
  simulation.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:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

Jun 24, 2021 9:06:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_60bc4990-975d-4014-bd23-317c28aec21a2313272796030296762

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg

Succesful model import: SBML file /tmp/temp421181789329182086.xml

final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.6.9

simulation_1.sedml/report

simulation_1.sedml/Figure_3b

simulation_1.sedml/Figure_3c

simulation_1.sedml/Figure_3d

simulation_1.sedml/Figure_3a

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (28.1 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.sedml/Figure_3a
  simulation.sedml/Figure_3b
  simulation.sedml/Figure_3c
  simulation.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:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

Jun 24, 2021 9:06:34 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_79ccd790-5456-4b89-83b6-f008907f1c897182841328847239653

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp7587270034617974416.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@101ca8da

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.6.9

simulation_1.sedml/report

simulation_1.sedml/Figure_3b

simulation_1.sedml/Figure_3c

simulation_1.sedml/Figure_3d

simulation_1.sedml/Figure_3a

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (12.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:04:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_fce8b000-35dc-4fda-a206-19e75d6529719001549274104559961

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp1258952234339334010.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@c1a4620

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (11.9 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:05:11 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5849bfe0-8166-4e9a-9d5c-84691f62cb713938248291956290890

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp5498658471573161323.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@c1a4620

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (11.9 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:05:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_95964d5c-30c0-44df-8ca0-8f7ec32afc7f7037709011324673693

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp5611209051782996532.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@c1a4620

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (14.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:05:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_dc767e95-640b-48be-9ffe-631631ed81a15173992221279483515

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7776705998215591823.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@c1a4620

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

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:

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:

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:

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:

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:

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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log:

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:

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:

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:

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:

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:

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:

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:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (3.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:00:32 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_760e0e5a-38fd-4613-8536-0f5ad4a312197273791312746720051

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (3.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:00:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_0a103ff5-d31c-4b05-826b-87b3074a04c74794201720967589201

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

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:

sedml.SimulatorProducesLogarithmic3DPlots (0.4 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:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (12.1 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:01:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_e37f7627-4038-4f88-b49c-45a6f1efffe27113611266525507715

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp447141541091651651.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4c5204af

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (13.2 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:01:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_f2b2de12-2707-446b-af1d-80e2d7409b437645413270686191771

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp8258310753009531827.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6a933be2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (15.3 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmph2ihyi7b/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:02:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_083fc742-b752-44a9-b40d-afb1c08ac38c6108360315547138429

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7826374998500697667.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5fa05212

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@26f1249d

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report__copy_2`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 165, in exec_sed_doc

    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')

  File "/usr/local/lib/python3.6/dist-packages/pandas/core/base.py", line 846, in to_numpy

    result = np.asarray(self._values, dtype=dtype)

  File "/usr/local/lib/python3.6/dist-packages/numpy/core/_asarray.py", line 83, in asarray

    return array(a, dtype, copy=False, order=order)

ValueError: could not convert string to float: 'NaN.9'

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (15.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp4epl49tm/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:02:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_08aecbb9-dcdf-46d6-9f45-f9372b59e7f52422524762313865176

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp3117684816092554382.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3f3ddbd9

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@9fecdf1

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report`.

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 307, in gen_plot_pdfs

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 283, in get_report_dataframes

    report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 357, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 145, in exec_sed_doc

    data_set_df = pd.read_csv(report_filename).transpose()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (13.1 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:02:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3104c6d7-2b6a-4a77-9ba9-3eca14ae1d8c3925049809403512838

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp3928910289497984157.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@bdecc21

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

BIOMD0000000912_sim.sedml/report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (5.9 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps67zebo7/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:36 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_740a0cb9-da7f-4127-9550-9fa97886b102754147786930573304

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_740a0cb9-da7f-4127-9550-9fa97886b102754147786930573304/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ee495307-9abb-4279-89e4-abb97f3eb9a07388724552842999574

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_ee495307-9abb-4279-89e4-abb97f3eb9a07388724552842999574/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (5.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpf2_nizp2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:42 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6fff091b-cdde-4f09-853b-aa0f8df6bd582210527704054671662

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_6fff091b-cdde-4f09-853b-aa0f8df6bd582210527704054671662/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:45 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_c0a2c24f-e9ba-4a81-8bb8-867c4eb12db15498869857038614101

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_c0a2c24f-e9ba-4a81-8bb8-867c4eb12db15498869857038614101/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.8 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3iwenrw0/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:48 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_9c302494-5379-4d0b-975d-de7c75bda1f75636910532411331773

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_9c302494-5379-4d0b-975d-de7c75bda1f75636910532411331773/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.8 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpmk9h5en5/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_21266d33-9804-405e-98d2-33fe440523b14576831892385259782

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_21266d33-9804-405e-98d2-33fe440523b14576831892385259782/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.8 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp9kjbrs95/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_012d06c8-d0c6-4bf1-98e1-6376c94374161567930081803875017

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_012d06c8-d0c6-4bf1-98e1-6376c94374161567930081803875017/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.8 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp1tb09cfw/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_4363d231-e869-4091-8899-1cf1d25deebf2019309761035227789

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_4363d231-e869-4091-8899-1cf1d25deebf2019309761035227789/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.8 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpc397ki2e/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 24, 2021 9:03:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp ...

- 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 [here](https://github.com/biosimulators/Biosimulators/actions/runs/969342676). 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/969342676).