'file' does not exist error when running gpt

When I try to run the gpt with an xml graph, I get the following error:

SEVERE: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Failed scan for Tools descriptors: I/O problem: /home/me/snap/java

Error: [NodeId: Read] Specified ‘file’ does not exist

There is no /home/me/snap/java file or directory. I have tried reinstalling the program, do I need to reconfigure java somehow?

A contributing problem is that I only have access to the computer through the terminal, so I do not know if snap desktop works.

This error does not harm your use case. See here:

Since yesterday there is an update available. Since you don’t have access to the Desktop you are not informed about updates.
But you can check for updates and install them from the command line. See Update SNAP from the command line

This is really an error. It seems that you have a problem in your graph or with the parametrisation from the command line.