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SelectVariants halted without an error

SystemSystem Administrator admin
This discussion was created from comments split from: GATK v4.1.3.0: Error with SelectVariants.

Comments

  • xiuczxiucz Member

    @bhanuGandham
    When I used this command, it failed sometimes(not all samples). It blocked here. Do you any suggestion?

    ~/gatktools/gatk-4.1.3.0/gatk SelectVariants \
    -R ~/hg19/gatk_bundle/ucsc.hg19.fasta \
    -select-type INDEL \
    --variant mutect2_twicefilter.vcf \
    -O indel.vcf
    
    
    21:58:54.712 INFO  SelectVariants - Done initializing engine
    21:58:54.772 INFO  ProgressMeter - Starting traversal
    21:58:54.773 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
    22:02:03.964 INFO  ProgressMeter -       chr19:15311618              3.2                  1000            317.1
    

    Thank you.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @xiucz

    I created a new thread for this question because the previous one was getting very long.

    Getting back to your error, I have a couple of questions to narrow down the issue:
    1. Try to rerun the command and let me know if it gets blocked again. It could possibly be a transient error.
    2. What are the specs of the machine you are using? It is possible the tool is running out of memory. Specify memory allocation with -xmx argument, and set it to ~ 2gb less than the total memory of the machine. You must always leave about 2gb for GATK native java code.

  • xiuczxiucz Member

    @bhanuGandham
    Thanks for your response, I have created a issue here https://github.com/broadinstitute/gatk/issues/6291#issuecomment-559330938.

    1, I have tried to rerun many time, but it still gets blocked.

    2, I used a HPC machine, and I specified the java memory to 40g, but it still got stocked. Actually, I had the same problem last year but not the same file, I finally got the result with a big memory of 200g !

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @xiucz

    Thank you for the update and for posting the issue ticket here, now other users can glean for it too!

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