DEseq2 error: unexpected symbol

I have been following the pathway HISAT2->StringTie->StringTie merge->Gff compare->FeatureCounts->Deseq2 for my RNA-seq analysis, as described in here:
Everything worked nicely, but at the level of differential expression, DEseq2 is giving this error:

Error in parse(text = x, keep.source = FALSE) :
:1:4: unexpected symbol
1: ~ 1X2X3XvsX4X5X6
Calls: as.formula … formula -> formula.character -> formula -> eval -> parse

Any idea what could have caused it and how to fix it?

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Hello @dotkom

Odd error. First, double-check that you executed the tutorial instructions exactly. Clicking on the rerun (double-circle) icon per dataset will allow you to review the settings actually used at each step.

If that doesn’t resolve the problem, write back and we can follow up. Note:

  1. Where you are running the tutorial (public server? URL? Other?)
  2. If you are using the tutorial data or your own.
  3. If versions of the tools used differ from any of those in the tutorial.

From an initial guess, this appears to be a problem with the reference annotation or some of the inputs were mixed up, but that is not certain yet.