Common errors

From time to time you’ll come across error messages in Janis, and hopefully they give you a good indication of what’s happened, but here we’ll address some.

If you’ve got a strange error message and don’t know what’s happening, post a message on Gitter or raise an issue on GitHub!

Command line positions

Command line positioning can be a little confusing. When running or translating you should follow this format:

janis run [run-arguments] [workflow-inputs]


  • run-arguments are options like --inputs, --recipe, --hint, --engine, --stay-connected, etc.
  • workflow-inputs are additional inputs you


  • There were unrecognised inputs provided to the tool “yourtool”, keys: engine, recipe, hint, otherkey
    1. In the command line, you might have accidentally placed a run argument in the workflow inputs section. Eg: :
      • Wrong: janis run yourtool --engine cwltool
      • Correct: janis run --engine cwltool yourtool
    2. You might have also included workflow inputs that yourtool did not recognise. Please ensure that yourtool accepts all the unrecognised keys.

Finding files

Janis looks in a number of places outside just your current directory to find certain types of files. Janis will look in the following places for your file:

  • The full path of the file (if relevant)
  • Current directory
  • $JANIS_SEARCHPATH (if defined in the environment).

If your path starts with https:// or http//, the file will be downloaded to a cache in the configuration directory (default: ~/.janis/cache) and will not go through the search path procedure.

You can run your command with janis -d yourcommand and look for the following lines which tell you how Janis is searching for files:

[DEBUG]: Searching for a file called 'hellop'
[DEBUG]: Searching for file 'hellop' in the cwd, '/path/to/cwd/'
[DEBUG]: Attempting to get search path $JANIS_SEARCHPATH from environment variables
[DEBUG]: Got value for env JANIS_SEARCHPATH '/path/to/janis/', searching for file 'hellop' here.
[DEBUG]: Couldn't find a file with filename 'hellop' in any of the following: full path, current working directory (/path/to/cwd/) or the search path.
[DEBUG]: Setting CONSOLE_LEVEL to None while traversing modules
[DEBUG]: Restoring CONSOLE_LEVEL to DEBUG now that Janis shed has been hydrated
# It's now searching the registry and will fail after it can't find it.


  • Exception: Couldn’t find workflow with name: myworkflow

    This might occur during a run or translate. Janis couldn’t find myworkflow in any of the usual spots, nor in the tool registry.

    • If you’re referencing a Python file (eg:, try giving the full path to the file or ensure that it’s correctly in your search paths.
    • If you’re referencing a tool that should be in the store, check the spelling of the tool. The name you reference needs to be the ToolId (under def tool(): return "toolid").
    • If you’re referencing a tool that you’re putting into the store, ensure there are no syntax / runtime errors in the Python file. You can double check this a few ways:
      • Running janis translate /path/to/your/ wdl and ensure that runs correctly.
      • Adding an if __name__ == "__main__": YourWorkflowClass().translate("wdl") to the bottom of your python file, then running python /path/to/your/ and checking that it translates correctly.
  • FileNotFoundError: Couldn’t find inputs file: myinput.yml

    This is likely because your inputs file myinput.yml couldn’t be found in the search path. Try giving the full path to your file.

  • Unrecognised python file when getting workflow / command tool: :: $PYTHONERROR

    This error results in a couple of ways:

    • There was a problem when parsing your file ( The error (given by $PYTHONERROR) was returned by Python when trying to interpret your file and get the workflow out. This could be syntactic or runtime error in your file.
    • You were looking a tool up in the registry, but you had a file / folder in your search path that caused a clash. You can include the --registry parameter after the run to only look up the tool in the registry.
  • There was more than one workflow (3) detected in ‘’ (please specify the workflow to use via the --name parameter, this name must be the name of the variable or the class name and not the workflowId). Detected tokens: ‘HelloWorkflow’ (HelloWorkflow), ‘HelloWorkflow2’ (HelloWorkflow2), ‘w’ (HelloWorkflow)

    When looking for workflows and command tools within the file, Janis found more than one workflow / command tool that could be run, in this case there were 3:

    • HelloWorkflow (HelloWorkflow)
    • HelloWorkflow2 (HelloWorkflow2)
    • w (HelloWorkflow)

    You need to specify the --name parameter with one of these ids (HelloWorkflow, HelloWorkflow2 or w) to run / translate / etc.

  • ValueError: There were errors in 2 inputs: {’field1’: ‘value was null’, ‘field2’: ‘other reason’}

    One or more of your inputs when running were invalid. The dictionary gives the field that was invalid (key) and the reason Janis thinks your value was invalid (value).


  • Exception: The tool ‘MyTool’ did not have a container. Although not recommended, Janis can export empty docker containers with the parameter allow_empty_container=True or --allow-empty-container

    One of the tools that you are trying to run or translate did not have a container attached to this. In Janis, we strongly encourage the use of containers however it’s not always possible.

    To allow a tool to be translated correctly, there are two mechanisms for doing so:

    • Translate without a container
      • CLI: Include the --allow-empty-container flag, eg: janis [translate|run] --allow-empty-container mytool
      • API: Include allow_empty_container=True, mytool.translate("cwl", allow_empty_container=True).
    • Override the container
      • CLI with the syntax: janis [translate|run] --container-override 'MyTool=myorganisation/mytool:0.10.0' mytool
      • API: include container override dictionary: mytool.translate("wdl", container_override={"mytool": "myorganisation/mytool:0.10.0"}), the dictionary has structure: {toolId: container}. The toolId can be an asterisk * to override all tools’ containers.