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What happend when I use gatk HaplotypeCaller, it become very slow.
When I use gatk HaplotypeCaller, I got this error:
WARN IntelPairHmm - Intel GKL Utils not loaded
WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
I can run HaplotypeCaller normally before, since I got this , the progress became twice slower. I am sure my CPU support AVX instruction.