Hi @joyhenart
The job is overwhelming the cluster node. Working at VGP or EU might help, or you will need to adjust the analysis.
Do you want to share this job, and the inputs? I can help to determine what is going wrong.
It sounds like this is not going to be enough (not enough genes called), and potentially has a lot of noise (why the files are too large to work with), and getting the protein alignment to work will help.
In short, you will want to annotate with ESTs and proteins first, then flow down into downstream steps. Maker will be run several times, layering in more annotation based on the prior annotation at each round. The computation is too much all at once.