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printReads performance : material consideration

sletortsletort franceMember
edited February 2015 in Ask the GATK team

Hi,
Here I have no problem :)

I ran a bqsr workflow on 2 set of data that were almost similare (same study, 2 indiv.), on 2 different machines.

Here are my observations :
set1 : Dell powerEdge R820, with 128Go Ram,
printReads ran in 7h hours with ~35Go ram used.
set2 : Dell powerEdge R730 with 193Go ram (and many jobs already running)
printReads ran in 1h20 min with ~35Go ram used.

Both sets were launched with the exact same command : -nct 20
set2 output is a little bigger (16Go vs 14Go for set1).

I'd like to know if this huge difference in duration is mostly due to materials, and if it is, which part ?
CPU speed, cache, ram access ?

Thanks

Answers

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