Bernadette Johnson

Hello! I do not have a solution for you; however, I would like to add that I have had a similar issue and found out what might be causing it....

There might be some formatting issues with your all_gtf_3.txt file. Does it look something like this? sample1 path/to/sample1_merged.gtf sample2 path/to/sample2_merged.gtf sample3 path/to/sample3_merged.gtf sample4 path/to/sample4_merged.gtf