Question: DEXSeq 1.26.0 running very slowly (stuck?)
0
10 months ago by
United States
Lance Parsons0 wrote:

I'm trying to get DEXSeq to run in Galaxy. I'm able to get the older version 1.24 to run in Galaxy, however, due to DEXSeq - dexseq_count.py issue the generation of the HTML reports would fail. So, I updated the Bioconda package to the latest supported by Bioconda (1.26.0) and updated the DEXSeq Galaxy wrapper.

The tests for the Galaxy wrapper seem to run fine, however, when I try to run DEXSeq on real data, version 1.26.0 runs for more than a day without completing (and then gets killed by our scheduler). Running version 1.24.0 on the same data finishes in about three hours.

Are there any known issues in 1.26 that would cause this? Any ideas on troubleshooting this? Perhaps options to change? Thanks for any advice.

dexseq • 253 views
modified 10 months ago • written 10 months ago by Lance Parsons0

Hi Lance. Do you know at which step it is getting stuck?

No, at the moment I don't know. However, it does not appear to be related to the report generation, since I've tried both with and without it, and it's still not finishing in a reasonable time. I haven't had the chance to extract everything and setup a run "manually" to try and replicate this yet. Just thought I check to see if there was anything that changed from 1.24 to 1.26 that would be a likely culprit.

OK, looking into this further, the problem comes when I enable multiple threads. It's fine as long as I only use one thread. The older version (1.24.0) worked fine with multiple threads, but isn't able to produce an HTML report (due to bugs in the conda package). So, for now I've got a workaround, but it'd be nice to get to the bottom of this. I suppose it's possible the issue is when the report is generated with multiple threads (though I'm not sure that the threads are used for that...).

Thanks for following this Lance. Do you get this problem in general when you use multiple threads? Or only when you specify multiple threads for DEXSeq?

Only for version 1.26.0 of DEXSeq. The Galaxy wrapper is here, btw: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq. The dexseq.R file. The GALAXY_THREADS variable is what controls the threads.