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-nct > 8 makes printreads slower (in apply-bqsr)?

jyjungjyjung Harvard Medical SchoolMember

Hello,

I am trying to test -nct parameter in printreads (bqsr). My machine has 32 cores (aws cc2.8xlarge) and input is a single BAM. So I tried "-nct 32" first, but it was almost as slow as "-nct 1". Actually any -nct >8 made it slow, so I am wondering if it's my fault or known/expected result. Thanks!

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