Question: Deseq2 with 0 lines in output
gravatar for ewalker
6 months ago by
ewalker30 wrote:


Using Galaxy main I have been happily runnning Salmon followed by Deseq2 to get normalized counts on some small RNAseq data. Up until Mon 21 May 07:37:49 PM(UTC) all ran just fine. But the next time I tried to use Deseq2 on a different Salmon set at 8:20:28, I got an empty file as a result (0 lines). Repeated rerun of Salmon and deseq2 have resulted in the same. I have searched through every parameter, and have not done anything differently, and have reached the end of my own troubleshooting capabilities.

Weirdly, if I rerun that Deseq2 job from Mon 21 May 07:37:49 PM(UTC), it returns the data just fine like it did the first time. It seems like there is something changed about how Salmon output happens now, since my 'old' Salmon outputs (from earlier yesterday) work in Deseq2 but my newer Salmon outputs won't work, and give 0 lines after running Deseq2.

Thanks for any help you can give.


salmon deseq2 • 258 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by ewalker30
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This sounds very much like a bug. We are finalizing the 18.05 release and would like to make sure this is not a native Galaxy problem versus a tool bug.

Would you please send in a shared history link to from your registered account email address? It is important to make sure all datasets are left undeleted.

In the same email, describe the data/tool combinations (briefly) and attach to a dataset number -- some matrix like the one below. Just reference one dataset per output to keep it simple, even though there can be multiple produced by the tool per job. The rest we'll be able to trace back to the input datasets used, tool versions, etc to find out what is going on.

new input/old output (N)
new input/new output (N)
old input/old output (N)
old input/new output (N)
* where "N" is the output dataset number

How to report a bug:

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k

Done. Thank you, Jen

ADD REPLYlink written 6 months ago by ewalker30
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