DexSeq runtime problem

usegalaxy.org support
1

Hello everyone,
I have recently been working on an RNAseq experiment and have been using Galaxy to do the analysis.

So far I have:

  1. Mapped the reads to the Drosophila genome using STAR
  2. I’m interested in looking at exon usage using DexSeq, so I next used DexSeq to prepare the annotations and then also successfully completed DexSeq-count.
  3. Finally, I tried to complete the DexSeq analysis with the list of counts from DexSeq-count. However, this initially failed because of a walltime error (I guess it was taking too long to run). I decided to try using a different server (cluster?) for this analysis so I switched over to the TACC Stampede 2 SKX partition since it seemed to allow for slightly longer runs. I ran a test run on the “Test/Development” partition and that worked fine, but I was thinking that this was perhaps a partial analysis, so I reran the DexSeq again using the main (i.e. non development/test) partition of the TACC Stampede server. The only difference between these two runs in terms of inputs is that on the second I asked DexSeq to output a file to visualize the results and in the first “test” run I did not.

This job has now been running for over a week and I can actually see the data online if I click on the little eye button, but since the job is still running I can’t download anything or export if from Galaxy. There’s no option to do that.

So I’m wondering…
a)will the TACC server eventually finish my job or should I somehow cancel the job? The wall time for that server according to Galaxy Main public site is 48 hours and I’m well past that now. Will it just keep running until it eventually finishes? If it finishes in error will I still be able to download the data that I can see now?
b) Is there a way to tell whether the data I was able to get from the “test/development” run that I did initially is complete? I can download that file from my galaxy history just fine but don’t want to use it if it isn’t complete.

Thanks so much for any help you all might be able to give.

2

For anyone that might have stumbled upon this question. I think the main issue I ran into was with the visualization of the results. Using the TACC server I reran DEXSeq with my samples, but omitted the “visualization of results” option and this worked fine. I was able to output a spreadsheet that had the exon usage in it for further analysis. I still don’t know if the “test/development” run I did was a complete analysis, since I used the non-developmental partition when I reran the job (without visualization).