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GenomicsDBImport bus error

HeqiangHeqiang KoreanMember

Hi,

I am a new user for gatk4. Recently I tried to combine 800 g.vcf files. It is quite slow by directly use 'CombineGVCFs', so I tried to use 'GenomicsDB' to make cobimed db file first. While after running few day, I just check the log file it is showd '3410 Bus error', what's the meaning of this error and how to solve it?
By the way, I want know is there any better method to combine g.vcf files more faster?

Thank you!

Qiang

Best Answers

Answers

  • HeqiangHeqiang KoreanMember

    Hi Bhanu,

    Thank you for your reply. My command as follows

    The log file as follows

    line 801 is the last line of my scripts.

    Thank you

    Qiang

  • HeqiangHeqiang KoreanMember
    edited November 2018

    Hi Bhanu,

    Thank you for your reply. But I checked our server, the free memory was over 2TB.

    Since I tried 120G before, it was showed that the memory not enough for my data. Anyway, I will reduce the Xmx to 200G to run again. Let's see what will happened.

    Thank you.

    Qiang

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Heqiang

    Yes please let me know.

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