We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple thr

Hi

I ran mutect2 with multiple threads (nct = 4) and confused with the INFO, Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option. The result of mutect2 would be different between single thread mode and multiple threads mode?

Thanks

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Yingya
    Hi,

    Are you asking if the results of MuTect2 will be different or if the runtime will be different with nct>1? Or, did you get an odd error when you ran with -nct 4? If you got an error or warning message,can you please post the entire message?

    Thanks,
    Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    edited December 2015

    Actually this message relates to computational performance, not accuracy. The software has some options to profile resource usage (like cpu, memory etc) but those can't be applied when multithreading for technical reasons.

  • YingyaYingya Member

    @> @Sheila said:

    @Yingya
    Hi,

    Are you asking if the results of MuTect2 will be different or if the runtime will be different with nct>1? Or, did you get an odd error when you ran with -nct 4? If you got an error or warning message,can you please post the entire message?

    Thanks,
    Sheila

    Sorry for no clear question! No, I did not get errors when I ran MuTect2. I am just confused about the difference between multiple threads mode and single thread mode on PairHMM. And if the variants result would be different between multiple threads mode and single thread mode?

    Thanks.,
    Yingya

Sign In or Register to comment.