Question: DeSeq2 still churning
0
gravatar for rodriguezk
8 months ago by
rodriguezk0
rodriguezk0 wrote:

Hi, I started my DESeq2 jobs on Friday afternoon and they are still churning. Is that normal? Should I stop them and start again? I initially received an error "Required metadata values are missing. Some of these values may not be editable by user. Selecting "auto-detect" will attempt to fix these values. I did that and I get the message "Metadata is being autodetected" when I click on the eye icon. thanks, Karl

usegalaxy.org deseq2 galaxy • 251 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by rodriguezk0
0
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There may have been a problem during job execution leading to a metadata conflict. This is usually a transitory server side issue.

I see the auto-detect for metadata running on several datasets. After two hours, these should have completed.

Permanently deleting those results/datasets and rerunning DeSeq2 is probably the best way forward. If the jobs end in an odd state again (metadata problems or other), please write back leaving those datasets intact (not deleted, not auto-detected) and we can follow up on what the problem may be. The inputs look OK from a quick review.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
0
gravatar for rodriguezk
8 months ago by
rodriguezk0
rodriguezk0 wrote:

I received errors again. Just the message " there are errors with this dataset" I ran mean, parametric, and local fit. Maybe I should not run them at the same time?

ADD COMMENTlink written 8 months ago by rodriguezk0

I'll take a quick look. Feedback soon. -Jen

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k

Each individual job only uses a single fit type, so that parameter is not a factor in the failures.

I do see two problems and both need to be corrected:

  1. One of the input htseq_count datasets is empty (dataset 9). This should be recreated with the proper inputs available in the history during execution.

  2. The primary factor label's name was entered as two words. This tool works best when a single alphanumeric "word" is used for factor labels (any - primary or sub-levels). Extra advice: avoid starting factor labels with a number (that can trigger a different error).

Please correct, rerun, and let us know if you still have problems. Thanks!

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
0
gravatar for rodriguezk
8 months ago by
rodriguezk0
rodriguezk0 wrote:

OK. Redoing htseq on that bam file. After that I will restart DESeq2 and let you know if that and #2 fix things

ADD COMMENTlink written 8 months ago by rodriguezk0
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