bwa sampe time to run

[Benjy]

Hello,

I have fastq files that are about 9GB each. (72bp paired end reads) aln on 7 threads (default parameters, seed length 72) takes about 2 hours to complete for each fastq which I can live with, but the sampe step is just too slow, it has taken 17 hours to process 14 million sequences. I've checked the insert size and it looks normal (less than 600 bp.). Is this performance normal?

Thanks,
Benjy

[Torst]

In my experience, yes, the "sampe" step is a bottleneck, whereas the "aln" step is really fast. Frustrating.

The main problem is disk i/o speed, especially if you are reading from and writing to a shared low performance disk.