Running EBSeq on many samples

[Elisabeth Heuston]

Hi EBSeq Users group!

I am new to these types of data analysis and have been learning through trial an error. I am trying to calculate differential expression on 10 samples, each with 2 or 3 replicates (23 samples in total). I've repeatedly tried to run EBSeq using the rsem pipeline, each time increasing computer resources, but after 10 days the job times out (no errors reported). I know I must be doing something wrong, but I can't figure out what the problem is. 

My command is:

rsem-run-ebseq MySamples.counts.matrix 2,2,2,2,2,2,3,2,2,2  MySamples.results

I am running rsem 1.3.0 on a Linux cluster, and have given it up to a 1T of memory. The program seems to be running on a single thread.

If anyone has any advice, I'd greatly appreciate it!

Thanks,

E