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Old 11-04-2011, 02:44 AM   #3
Location: Seoul, South Korea

Join Date: Oct 2011
Posts: 30

Originally Posted by raonyguimaraes View Post
No it shoudln't take that long ... but this is proportional to your computer's capabilities ... What is your config (specially processors)? Are you using threads in GATK ? How many ?
model name : AMD Opteron(tm) Processor 6172
cpu MHz : 2100.034

I think samtools sort takes so long probably because I divided my .bam alignment output into 500 pieces... (before alignment and the output is still divided)

There are 48 cores; I gave -nt value 24, but it seems to utilize about 6 cores.
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