StringTie error generating gene and transcripts counts files

Hello. I’ve been running tools on Galaxy today to analyze bulk RNA-seq data following this pipeline ( I’ve run StringTie on two different datasets and I keep getting this error while trying to generate the Gene and Transcript counts files.

Dataset Error Report

An error occurred while running the tool Details

Tool generated the following standard error:

/usr/local/bin/ SyntaxWarning: invalid escape sequence ‘-’
RE_COVERAGE=re.compile(‘cov “([-+\d.]+)”’)
/usr/local/bin/ SyntaxWarning: invalid escape sequence ‘-’
RE_GFILE=re.compile(‘-G\s*(\S+)’) #assume filepath without spaces…

I have sent a bug report to the Galaxy administrator but while I wait for their reply, I was wondering if anybody else has faced the same problem or if somebody has some answers. Is this an issue with my dataset or with the StringTie tool?

Hi @tanvirai

This help will apply for you, too.

Right now, you are calling counts against a single output from a single Stringtie run (scientific problem), and the option to call new gene models is still on (technical problem).

Hope this helps, and thanks for sending in the bug report for supporting data, very helpful! :slight_smile:

Thank you!!

1 Like