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Mutect2 stops with no log files

SystemSystem Administrator admin
This discussion was created from comments split from: Error in Mutect2.


  • liuxiangliuxiang Member
    edited April 2019
    I am sorry I cannot post discussion so I have to ask here.

    GATK4.1 Mutect2 work for long time but no output

    I use Mutect2 to call variants. I submit my scripts to PBS system and operated for over 48h but with no vcf output and no error log.I checked all bam are sorted, indexed and validated.All reads group are accordanced. But it just like stop at "09:06:16.068 INFO Mutect2 - Initializing engine" in log file.

    I want to know, is it normal phenomenon costing so much time without nothing output, even no vcf header ?
  • bshifawbshifaw Member, Broadie, Moderator admin

    No this isn't normal. You'll probably need to check the compute resources given to the submitted job to make sure it has enough disk, memory, etc resources available. Also try running the script without PBS to make sure PBS isn't causing the unexpected job to stop unexpectedly.

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