Question: DEXSeq memory issue
gravatar for Anil Kesarwani
5.7 years ago by
United States
Anil Kesarwani90 wrote:


I am using DEXSeq v1.12 on R 3.1.1 to perfom analysis with total 573267 exons for their diffrential usage between 5 healthy and 8 patient samples (each  ~10 GB BAM file from TopHat).

The job is termintated as memory exceeds the limit (~270 GB RAM). Is there any way to handle scalability of DEXSeq.

Using BPPARAM function in DEXSeq, I tried to submit the job on 10 nodes (each with 8 processors and 36 GB RAM), but the job is getting terminated with the following message:

Aborted by PBS Server
Job aborted on PBS Server initialization
Exit_status=-4 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:11:58 Error_Path=/dev/pts/0 Output_Path=/dev/pts/0

It appears that DEXSeq is not distributing the job across the nodes.

I am having big trouble with doing dxd = testForDEU( dxd, BPPARAM=BPPARAM), which highly memory intensive step of DEXSeq.

Could somebody please guide me if there is any better way of running this program. Any suggestion is highly appreciated.





rna-seq dexseq • 1.4k views
ADD COMMENTlink modified 5.7 years ago by Devon Ryan98k • written 5.7 years ago by Anil Kesarwani90
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