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GenomicsDBImport error: File2TileDBBinaryException

jhbjhb Member

Hello, I've been trying to get the HaplotypeCaller-in-gVCF-mode to work for a combination of exome samples, some of which are diploid individuals, and others of which are bulks with ploidies ~20. For about 20% of my chromosomes, The GenomicsDBImport step fails, with the following error message:

09:58:45.656 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
09:58:46.530 INFO  GenomicsDBImport - Importing batch 1 with 6 samples
terminate called after throwing an instance of 'File2TileDBBinaryException'
what():  File2TileDBBinaryException : read_one_line_fully && "Buffer did not have space to hold a line fully - increase buffer size"

I'm not sure what this means, and a google search brings up next to nothing.

I am working with mosquito exome data, 150bp PE illumina reads, GATK 4.1.3.0, java 1.8.0_181. I've been following the Broad best practices pretty closely, although I haven't managed to figure out how to bootstrap base recalibration yet.

Example GenomicsDBImport command:

gatk --java-options '-Xmx5G' GenomicsDBImport \
        --genomicsdb-workspace-path ../vcfs/combined_gvcfs/NW_021837046.1 \
        --intervals NW_021837046.1 \
        -V ../vcfs/gvcfs/BH2.gvcf \
        -V ../vcfs/gvcfs/BH3.gvcf \
        -V ../vcfs/gvcfs/K01.gvcf \
        -V ../vcfs/gvcfs/K02.gvcf \
        -V ../vcfs/gvcfs/M01.gvcf \
        -V ../vcfs/gvcfs/M02.gvcf 

Issue · Github
by bhanuGandham

Issue Number
6150
State
open
Last Updated
Assignee
Array

Best Answer

Answers

  • jhbjhb Member

    I should also mention: I played around with increasing "--genomicsdb-segment-size" and "--genomicsdb-vcf-buffer-size", as well as the amount of memory available to java. Increasing any or all of them by a factor of about 10 had no effect, always producing the same error.

  • bhanuGandhambhanuGandham admin Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @jhb

    I am looking into this and will get back to you shortly.
    Would you please share with me the specs of the machine you are running these tools on. It will help us narrow down the issue.

  • bhanuGandhambhanuGandham admin Cambridge MAMember, Administrator, Broadie, Moderator admin

    @jhb Are you running this on a NFS(Network File System) ?

  • jhbjhb Member

    I don't know what a network file system is--is that a synonym for a cluster? If so, then yes. If not, then I'm not sure: how do I tell?

    The nodes I'm running on are either 1) 2 x 8-core Intel Xeon E5-2680 or 2) 2 x 10-core Intel Xeon E5-2680 v2. Either way, I'm using a single core with 30 GB memory. x86_64 GNU/Linux architecture. Is this useful? Please let me know if there is any more information that I can provide.

    Thanks for your help!

  • jhbjhb Member

    Additional information: the bulks seem to be the root of the problem, as running GenomicsDBImport only on the diploid individuals of the sample set produces none of these errors.

  • bhanuGandhambhanuGandham admin Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @jhb

    This error requires adjusting the buffer size, but unfortunately that option is not available in GATK. I have created a github issue ticket to fix this. You can follow progress on this issue here: https://github.com/broadinstitute/gatk/issues/6150

  • jhbjhb Member

    Thanks a lot, I'll give that a try and report back!

  • jhbjhb Member

    It worked, thanks!

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