# Troubleshooting¶

## Verbose and debug output¶

Biopax2Cadbiom comes with a build feature that can outputs a lot of debug information when enabled.

Logs are stored in /tmp/biopax2cadbiom.log on GNU/Linux. By default the logging level outputs only warnings and errors, but the verbosity can be increased with a similar command:

\$ biopax2cadbiom -vv debug ...


## Conversion issues¶

### Warnings and permanent nodes¶

During the conversion, some warnings with the following format can be generated:

WARNING: Reflexive transition: <ENTITY> -> <ENTITY> - This transition will not be taken into account.


This means that a transition reflects an autogeneration of an entity in the translated network. This is not usually supposed to happen and when the Cadbiom model is loaded, these transitions will not be interpreted.

During the development, these warnings help to solve and identify the unsupported cases of the BioPAX standard. However, in a release version, these are often inconsistencies in the BioPAX file. In the following you will find a number of real cases accompanied by explanations.

### Unsupported interactions¶

There may be errors related to the translation of some interactions defined in the BioPAX formalism.

#### Omitted reactions¶

Type of reaction is deliberately unsupported because it is too imprecise: <BIOPAX_URI>


According to the BioPAX standard [1], MolecularInteractions are produced by high throughput systems that does not satisfy the level of detail (i.e. enough experimental evidence) required to model them with ComplexAssembly class. These interactions will not be translated.

#### Unexpected reactions¶

UNEXCEPTED REACTION: <BIOPAX_URI>


During the development of Biopax2Cadbiom, we have never encountered this type of interaction in the databases used. These interactions will not be translated.

Footnotes

 [1] BioPAX – Biological Pathways Exchange Language - Level 3, Release Version 1 Documentation, 2010. Available: http://www.biopax.org/release/biopax-level3.owl