Troubleshooting.

step	problem	possible reason	possible solution
3,21	Error: “can not parse sbml model file”	The sbml model file does not exist or contains errors.	Make sure the model name provided in the input file (or command line) is exactly the same as the model file. If the sbml model file was manually generated, make sure all tags are correct and closed and only sbml standard acceptable expressions and syntax is used.
15,29	Error: “Please do not give empty strings for model names!”	The model names contain invalid strings.	Check the names of each provided model in the input file
15,29	Error: “The number of given prior distributions for model X is not correct”	The model contains a different number of parameters than was defined in the input file.	Provide one prior distribution per parameter defined in the model. If some parameters are known, they still need to be defined (as ‘constant’). Note: when using an sbml model file an additional parameter appears, which defines the compartment size. This parameter is always defined as ‘parameter 1’. For the vast majority of systems this parameter is constant 1.0
15,29	Error: “Please provide an initial value for each species in model X.”	The number of species in the model and in the input file does not correspond to each other.	Check the input file and make sure that the initial conditions are correctly defined. For each species in the model one initial condition needs to be provided. This can either be ‘constant’ if the initial condition is known, or one of the following, if the initial condition needs to be inferred: ‘uniform’, ‘normal’, ‘lognormal’.
15,29	Error: “The prior distribution of parameter X is wrong defined.”	Invalid expression in the input file.	Check the type of distribution for parameter X in the input file. Possible types are: “uniform”, “normal”, “lognormal” and “constant”.
15,29	Error: “The integration type for model X does not exist.”	Invalid expression in the input file.	Check the integration type for model X. Allowed expressions are “ODE”, “SDE” and “Gillespie”.
15,29	Error: “The results folder already exists.”	There is already a file/folder called ‘results’ in the working directory.	Either change the working directory, change the name of the existing folder or remove the folder.
15,29	Error: ”Please provide a fit instruction for each model”	Wrong or no fitting instruction is provided.	Always provide the same number of fitting instructions as provided time series (if the number of species differs from the number of data series). Fitting instructions can be simple expressions such as ‘species1’, but also more advanced instructions such as ‘species1+10*species3’. This is particularly useful when data need to be scaled or only combinations of species are observed.