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What does NSRuntimeProfile - Outside means?

Dear GATK team,

I am currently moving my pipeline from GATK 1.6 to GATK 2.2. SelectVariants now takes 30 min to run (instead of 1 min with GATK 1.6)! The runtime profile gives:
INFO 15:38:16,232 ProgressMeter - Total runtime 1841.63 secs, 30.69 min, 0.51 hours
INFO 15:38:16,232 NSRuntimeProfile - Input time: 21.8 s ( 1.19%)
INFO 15:38:16,232 NSRuntimeProfile - Map time: 22.6 s ( 1.23%)
INFO 15:38:16,232 NSRuntimeProfile - Reduce time: 0.4 s ( 0.02%)
INFO 15:38:16,233 NSRuntimeProfile - Outside time: 29.9 m (97.56%)

What does Outside means? Is that the writing time to disk?

The program writes to /scratch/local/.

In advance, thanks for your help.

Sylvain

Answers

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