Question: Error in Tophat
0
gravatar for radhika.patel
21 months ago by
United Kingdom
radhika.patel0 wrote:

Hello,

I have been trying to run the same workflow to convert FASTQ files to Tophat for a few weeks now but keep getting an error saying 'An error occurred setting the metadata for this dataset Set it manually or retry auto-detection'. I have tried setting it manually and doing auto-detection but nothing seems to work. Please could you inform me what I could do to resolve the issue?

Thanks, Radhika

ADD COMMENTlink modified 21 months ago • written 21 months ago by radhika.patel0
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

In the dataset, a link to auto-detect the metadata is displayed in a yellow box. Alternatively the pencil icon can be clicked on to reach the Edit Attributes forms. On the first tab is an "Auto-detect" button. Both do the same thing.

This is a known issue specific to Tophat accepted hits output. Our team is working to correct the issue, but it is somewhat complicated to resolve, and no timeline for the fix is available yet.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
0
gravatar for radhika.patel
21 months ago by
United Kingdom
radhika.patel0 wrote:

Thanks for the reply. I have been trying the auto-detect button but the error still remains saying the metadata is used as input or output and it still doesn't run the job. Is there an alternative workflow I could try for this?

Thanks, Radhika

ADD COMMENTlink written 21 months ago by radhika.patel0

The auto-detect must be run on the dataset before running other jobs.

Any downstream jobs started already will just fail anyway - so it is Ok to delete them. Give this a few minutes to process in the database. Then use auto-detect. When that completes, start up the downstream jobs again.

If necessary, workflows should be split into two parts - 1) those that execute tools through Tophat and 2) those that execute tools that use Tophat input. In between running the two, autodetect should be used.

This is a temporary problem and one we hope to correct soon, our team understands how this is inconvenient.

Jen

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson25k
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