Open alyxgray7 opened 2 years ago
Hello,
Following this thread. I encountered some issues when attempting to run the MPI version, specifically related to package compatibility. It seemed like DegNorm had a preference for Python 3.6, which didn't align with the Python version available on our clusters. Have you faced similar issues, and if so, how did you manage to resolve them?
At the end, I opted to use the standard version but it takes really long time!
Thank you!
Marcela
Hi Marcela @marce-sarrias,
We actually had our HPC staff build an environment that could run the MPI with a compatible Python version. Unfortunately, this was ultimately unsuccessful due to the memory issues that we were never able to resolve...
If memory serves me correctly, the standard version would also error out from the same resource issues. Our single successful run (I think with only 3 samples?) also took a very very long time! I'm glad to hear the standard version is working okay for you.
Best of luck, Alyx
Hello,
Thank you for providing this tool - we'll be working with 141 highly degraded (majority are RIN < 5.0) human RNAseq samples that would really benefit from this normalization approach. In preparation, we've been working with a publicly available RNAseq dataset (90 samples - GSE68086) and have run into a few problems testing the DegNorm MPI module. Even after reducing the number of samples to 6, we have run into the same set of memory errors.
Each HPC workflow was submitted across 4 nodes. We've tried submitting at a max of 20 cores/node and 264 Gb mem. Each job processes for ~ 14 hours and then errors out around the same spot with these two messages. I'm happy to provide you the full log files if that's helpful.
DegNorm command being used:
Thank you!
Alyx @FiReTiTi