Has anyone tried uploading a .txt tab-delimited file as an interval file and noticed that setting the attributes does not work as it did before the Galaxy update?
- I uploaded a .txt tab-delimited file as an interval file (headers: gene, locus, chrom, chromStart, chromEnd). In the preview, the data sorts nicely into 5 columns.
- I tried saving the following Attributes: comment lines = 1, chrom = 3, start = 4, end = 5, strand column (unchecked), name identifier column = 1.
- Then when I clicked Save, the strand column box checked itself.
- I unchecked both the Strand and Name Identifier (as an experiment) and clicking save re-checked both boxes.
I attempted to fix the problem by uploading a version of the file that has a strand column (headers: gene, locus, chrom, chromStart, chromEnd, strand). After setting the strand column to "6" I tried to run Join (under Operate on Genomic Intervals) with some ChIP intervals. The process keeps gettign stuck and I get no error messages.
Please help. Thank you.
Hello, How is the process getting stuck? Is the job grey? In "prep/new dataset" or "queued" state (noted in dataset comments)?
Thanks - a bit more information and we can help. If the job has already succeeded, that would be good to know.
Jen, Galaxy team
The job goes from grey to yellow ("This job is currently running") and then never finishes. I startied it again yesterday and after coming back to my office the next day I still see it running.