Question: BUG: Cannot save "unchecked" Strand and Name Identifier attributes for interval file
2
gravatar for karmella.haynes
22 months ago by
United States
karmella.haynes40 wrote:

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.

galaxy • 458 views
ADD COMMENTlink written 22 months ago by karmella.haynes40

Hello, How is the process getting stuck? Is the job grey? In "prep/new dataset" or "queued" state (noted in dataset comments)?

https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Thanks - a bit more information and we can help. If the job has already succeeded, that would be good to know.

Jen, Galaxy team

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson24k

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.

ADD REPLYlink written 21 months ago by karmella.haynes40
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Jobs have up to 48-72 hours to complete, depending on the cluster resource used. If a job is in a yellow execution state, it is best to allow it to finish. Restarting will place the new job back at the end of the queue, extending wait time before execution (grey queued dataset) and the time it takes to start up and execute completely (yellow processing dataset -> green successful dataset).

There were some more recent issues with the cluster resolved this morning. So, if datasets failed over the last few days (red), please rerun them now.

Thanks for your patience during this upgrade phase at http://usegalaxy.org

Jen, Galaxy team

ADD COMMENTlink modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson24k

Concerning the interval file upload/metadata issues:

I noticed some odd behavior with metadata assignments last week with this datatype. I believe these are resolved now, but let us know if not. If you still have an example of an uploaded file that has metadata assignment problems, please share that history with the dataset undeleted (how to: https://wiki.galaxyproject.org/Learn/Share). Include the dataset number, a link to this biostars post, and the shared history link in an email to galaxy-bugs@lists.galaxyproject.org.

It is OK if the interval dataset is in a new history containing just that uploaded file, it is enough to test this particular issue with. If you go this route, please also capture and send a screenshot of the settings used with the upload tool, or note what these were in the email.

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson24k

Thank you. The metadata problem is still there. I just sent the e-mail with all of the details and a shared history link. This issue is very annoying, especially since I have a similar interval file that seems to behave just fine (it does not force me to select Strand). This file was added a few months ago, before the Galaxy update.

ADD REPLYlink written 21 months ago by karmella.haynes40
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