Hi,

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.

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

Using BPPARAM function of 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 is a highly memory intensive step of DEXSeq.

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

Best regards,

Anil

Anil

thanks for your message. Can you:

• Upgrade to the most recent release version of R and DEXSeq - currently 1.14 (http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html ). Older versions are not supported.
• Send a reproducible example, and the complete output. You perceived "The job is terminated as memory exceeds the limit" but it would be good to see whether this is really the reason (a memory use of ~0.5 MB per exon would be quite spectacular) And if so, at what stage during the process, etc.

Best wishes

Wolfgang