Hello, I am doing some transcriptome assembly using Stringtie as well as other assemblers. I am running the assemblies with trimmed and filtered bam files and a reference genome. The other assemblers I am using are working fine with the SRA data I provide them. For some reason, Stringtie works about half of the time, and the other half returns this error "GffNameList Error: invalid index (-1) " and nothing else. I have looked at the documentation for the code and cannot make much sense of it, and there are no posts about this problem yet. I do not understand why about half of my data is running properly and the other half isn't using the same reference file.
Any help is appreciated,