I am using sequencing files and a GTF file that was generated. It works for regular counts but not when I ask it to generate de novo sequences. I just keep getting the fatal error. Can anyone help with this?
Hi @KMKLOHONATZ
Check this post: StringTie error generating gene and transcripts counts files
Hope that helps.
Kind regards,
Igor
HI @igor , that isn’t the same issue I am having. I want stringtie to create gene models using a reference annotation as well as any other models it can detect from that sample. I have no issues running stringtie with just using the reference genome. It is when I turn that option off I always get the fatal error code.
Hi @KMKLOHONATZ
This sounds like a problem with your reference annotation. You can try to run it through gffread to see if that helps to normalize the content.
You are also welcome to generate and post back a history share link to the error, or share it all in screenshots (don’t forget to expand the input datasets, and to capture the job logs!). Please see the banner topic at this forum, or here directly. → How to get faster help with your question
At a high level, these are the items we would help to check. In particular see the details about the expected content in reference annotation. → FAQ: Extended Help for Differential Expression Analysis Tools
You could also compare to the data we include in tutorials. The first two hands-on tutorials in here cover similar analysis to yours. → Transcriptomics / Tutorial List
Hope this helps, and let us know how this turns out! 