If your reads were not quality trimmed before assembly, then you should do that first.
Resources about the Trinity pipeline, include assembly statistics tools:
That said, I still think this could be a server-side issue. These tools were designed to work with data that isn’t “perfect”. You could also try alternative options than RSEM – Salmon or Kalisto as others needed to do (see the ticket that the Trinity authors wrote back on Trinity transcript_abundance.pl error using RSEM · Issue #305 · trinityrnaseq/trinityrnaseq · GitHub).
But if this is an actual cluster issue, those wouldn’t work either. In testing today, many tools that run on the same cluster as this one all failed. Our administrator is working on it.