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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

HaplotypeCaller Follow

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    Devendra Waikul

    I am helping setting up GATK4 pipeline. I am getting Java fatal error for individual chromosome intervals on genomicsDBimport. I am guessing I must have set the wrong output file extension for haplotypecaller output. 
    I have set the output to be vcf_haplotype_output = output_haplotype.vcf with flag set to -ERC GVCF

    Can anyone suggest what should be an output extension for this command?

     

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    Monete Rajão Gomes

    Hi Devendra,

     

    I think when you use -ERC GVCF option, your output should be "output_haplotype.g.vcf" or (better) "output_haplotype.g.vcf.gz"

    Like described above on session: Single-sample GVCF calling (outputs intermediate GVCF)

    Hope this helps.

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    Devendra Waikul

    Hello Monete Rajão Gomes,

    Thank you for providing the quick response. 

    I have one more question. Did you face java errors after the genomicsDBimport command?

    15:33:00.356 INFO ProgressMeter - Starting traversal
    15:33:00.356 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
    15:33:00.495 INFO GenomicsDBImport - Starting batch input file preload
    15:33:48.560 INFO GenomicsDBImport - Finished batch preload
    15:33:48.563 INFO GenomicsDBImport - Importing batch 1 with 31 samples
    03:08:43.526 INFO ProgressMeter - chr22:1 695.7 1 0.0
    03:08:43.531 INFO GenomicsDBImport - Done importing batch 1/1
    03:08:43.533 INFO ProgressMeter - chr22:1 695.7 1 0.0
    03:08:43.533 INFO ProgressMeter - Traversal complete. Processed 1 total batches in 695.7 minutes.
    03:08:43.533 INFO GenomicsDBImport - Import completed!
    03:08:43.533 INFO GenomicsDBImport - Shutting down engine
    [June 18, 2020 3:08:43 AM EDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 695.79 minutes.
    Runtime.totalMemory()=28427943936
    Tool returned:
    true
    #
    # A fatal error has been detected by the Java Runtime Environment:
    #
    # SIGBUS (0x7) at pc=0x00007fca5fb9d330, pid=388337, tid=0x00007fda500b6740
    #
    # JRE version: OpenJDK Runtime Environment (8.0_181-b13) (build 1.8.0_181-b13)
    # Java VM: OpenJDK 64-Bit Server VM (25.181-b13 mixed mode linux-amd64 )
    # Problematic frame:
    #

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    Monete Rajão Gomes

    Hi Devendra Waikul

    Unfortunately, I've never used genomicsDBImport before. I've been using combinegvcf, instead.

    Maybe you should look for this error in other sites or in read-only GATK v3 previous site.

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    Chunyang Bao

    Hi, 

    I can not find "--genotyping_mode" option in this version. Can I assume DISCOVERY mode is the default mode. But, I am wondering if "GENOTYPE_GIVEN_ALLELES" is still being supporated in this version. Any thought?

    Chunyang

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    Joy Bordini

    Hi there,

     

    I noticed that HaplotypeCaller detects different variants (and number of variants) when i run it with target file without scatter-gather approach compared to when i run it with scatter-gather approach. Is this behaviour related to some internal implementation? Any other suggestion?

     

    Thanks

    Joy

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    Matt Snyder

    I just ran HaplotypeCaller and got the error below. Clearly my input is not properly named. That is easily fixable and is not an issue. 

    A USER ERROR has occurred: Couldn't read file /home/dnanexus/inputs/input7167917857716864453/archive. Error was: The file /home/dnanexus/inputs/input7167917857716864453/archive exists, but does not contain Features (ie., is not in a supported Feature file format such as vcf, bcf, bed, or interval_list), and does not have one of the supported interval file extensions ([.list, .intervals]). Please rename your file with the appropriate extension. If /home/dnanexus/inputs/input7167917857716864453/archive is NOT supposed to be a file, please move or rename the file at location /home/dnanexus/inputs/input7167917857716864453/archive

    I just wanted to report a very minor "error" in this error message. "supported interval file extensions" should also include at least ".interval_list" if it is an exhaustive list. My HaploytpeCaller call with my -L file works with the Picard formatted interval_list. Not sure, so I thought I would bring it up for potential inclusion in a later release.

    Thanks for GATK! Love it!

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