Would you please create a history with just that failure, then share it back? Maybe there is a problem with some setting/option or an actual bug with the tool itself.
And … one troubleshooting tip – when uploading GTF data, leave all the options at default so that the file is uncompressed with the datatype gft detected and assigned when the data is added to a history. Setting the datatype manually can introduce a few problems. Maybe try loading the original file that way when creating the history that you are sharing. Plus, running the tool one more time with a freshly loaded file in isolation would eliminate any temporary reasons for the failure.