The tool annotateMyIDs does have a small problem right now (all versions). The tool is not ignoring header lines even when that is set on the tool form.
Cross-reference post: AnnotateMyIDs Fatal error
If that does not solve the problem, check that the Organism and ID Type are a match for the transcripts or genes in your data. The tool UniProt ID mapping and retrieval is an alternative for many use cases.
Which tool to use depends on where the existing annotation was sourced (meaning: what ID content they currently represent). The format of the transcript/geneIDs can also cause problems. I’ve seen problems come up when a version is added to the end of the value – that should be removed before using either tool if present. Example: NM_130786.2 should be modified to be NM_130786.
If this does not address your issue, please share a few of the IDs and the source/genome build of the reference GTF used with whatever counting tool you used as input to DESeq2. We can probably help with determining the right starting “ID” type.