Issue with StringTie Output File when using DESeq2 option

I am having issues running the StringTie after adjusting the settings. When I originally ran a workflow I created with StringTie as one of the tools, everything ran correctly. However, I modified the settings so that it would produce “Gene Counts” and “Transcript Counts” output files for differential expression. I did this by selecting " DESEQ2/edgeR/Limma-voom" as the option for the “Output files for differential expression.” When I changed this setting, I got an error (Fatal Error: Exit Code 1 () ). Also, despite all the files being red, only the Gene Counts and Transcript Counts files were unfilled. The other files generated were normal.

Does anyone know what could be giving me this error. If necessary, I can share my history.

Hi @tgray4
By any chance, have you submitted StringTie using two options, prediction of gene models and read counting, in the same job? I believe StringTie does not support this anymore. A proper workflow is: create gene models for every sample, merge individual gene models into a single “master” annotation using StringTie merge, and use the master annotation for read counting. The reads can be counted with StringTie or any other software, for example, featureCounts. For read counting with StringTie disable gene prediction. Read counting should be done with the same annotation, for sake of comparison, hence, the two options were made incompatible.
If I misunderstood the issue, share the history, so people can check what is going on.
Kind regards,

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Dear Igor,
When I use StringTie, of the three files generated, only Assembled transcripts are available (green), while Transcript counts and Gene counts both show errors (red). which showed that “Metadata generation failed. Please retry”, I sincerely ask you how to solve this problem. thank you
Kind regards,

I ran into the same problem as you when running StringTie, how did you solve it?

The instructions are above, also here

More details can be found in this other Q&A