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!

SelectVariants halted without an error

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


  • xiuczxiucz Member

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

    ~/gatktools/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

    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!

Sign In or Register to comment.