Hello.
I have ran Tophat for Illumina with groomed RNA-seq data and it is marked red and has an error "
long_spanning_reads".
What does this mean?
what should I do?
In addition, I then tried to report the error, but it consistently tells me 'Mail is not configured for this Galaxy instance"
What does this mean?
I am looking forward to hearing from you.
Thank you.
Rise Kum
Hello,
I believe this error means that the job required more memory than was available on the instance. There is some discussion about this at Biostars, SeqAnswers, etc. plus the release notes for Tophat explain a few issues with version and this function. Here is an example web site: http://ccb.jhu.edu/software/tophat/index.shtml
This is a local or cloud? Bug reporting is not on by default. If is your own Galaxy, then the reports would just go to you anyway.
You could try Tophat2 or adjust the parameters for this tool (after making sure it is the most current version without the known issues). Moving to a Galaxy with more dedicated memory is also an option.
Hopefully this helps, Jen, Galaxy team
