I am encountering an issue while running eggNOG-mapper on Galaxy.
Some protein-coding genes present in my input FASTA file (protein sequences) are missing from the final annotation output file. I have checked carefully and confirmed that these sequences are indeed present in the input FASTA, with proper headers and no obvious formatting problems.
However, these gene IDs do not appear at all in the eggNOG-mapper annotation output (TSV file). It is not a case of missing functional annotation — the genes are completely absent from the output file.
Could you please help me understand why this might happen?
Let’s break down how the tool is performing the analysis to narrow down what may be going wrong.
There are three components to this tool’s protocol. The first one is:
eggNOG Mapper search phase
Is this where your protein sequences are not gaining hits? Or did you pass through this step and the problem is happening with later steps and that is what you are trying to do?
Have you confirmed that those proteins are included in the annotation hosted? Or, did you expect your genes to be included and they aren’t capturing hits?
To start, I would suggest checking against the other online versions of the annotation. This would help to confirm if your queries are missing from the underlying databank in the set or not.
Keep in mind that you may need to adjust the parameters to capture a hit! The wiki above would be the best resource for investigating the best parameters for your samples.
From there, it is difficult to guess more! We can help to ensure that there isn’t a technical problem with the Galaxy implementation at the server you are working at if you would like to share back your history!
