I’m trying to run StringTie on Galaxy Europe. I gave the input as HISAT2 bam files and gtf reference annotation file as NCBI GRCh38.gtf (https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gtf.gz)
StringTie tool turns red immediately and gives this following error message:
Dataset Error Report
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1 .
Please help me. What do I do?
Update: I’m getting the same error with Trimmomatic as well!
## Dataset Error Report
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 .
Is something wrong with Galaxy tools or am I doing something wrong?