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CombineGVCF slowing down at certain region on chromosome 1



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    Update on the problem above.

    As smaller batches or selecting only one chromosome (using intervals option (-L)) did not speed up CombineGVCF, I decided to try GenomicsDBimport.

    I successfully created a GenomicsDB of the 36 samples for chromosome 1, using the following command:

    gatk GenomicsDBImport \
    -V output/B7_2.g.vcf.gz \
    -V (34 samples)... \
    -V output/B8_7.g.vcf.gz \
    --genomicsdb-workspace-path RC_chr1 \
    --intervals chr_1

    and would like now use GenotypeVCF on this GenomicsDB  using the following command:

    gatk GenotypeGVCFs \
    -R Reference/uT.fasta \
    -V gendb://RC_chr1 \
    -O RC_chr1_36samples.vcf

    but not get the following error:

    22:57:31.195 INFO  GenotypeGVCFs - ------------------------------------------------------------

    22:57:31.196 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.6.0

    22:57:31.196 INFO  GenotypeGVCFs - For support and documentation go to

    22:57:31.196 INFO  GenotypeGVCFs - Executing as xxxxx@galaxy on Linux v4.4.0-133-generic amd64

    22:57:31.196 INFO  GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01

    22:57:31.196 INFO  GenotypeGVCFs - Start Date/Time: 26 May 2020 22:57:30 CEST

    22:57:31.196 INFO  GenotypeGVCFs - ------------------------------------------------------------

    22:57:31.197 INFO  GenotypeGVCFs - ------------------------------------------------------------

    22:57:31.197 INFO  GenotypeGVCFs - HTSJDK Version: 2.21.2

    22:57:31.197 INFO  GenotypeGVCFs - Picard Version: 2.21.9

    22:57:31.198 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2

    22:57:31.198 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

    22:57:31.198 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

    22:57:31.198 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

    22:57:31.198 INFO  GenotypeGVCFs - Deflater: IntelDeflater

    22:57:31.198 INFO  GenotypeGVCFs - Inflater: IntelInflater

    22:57:31.198 INFO  GenotypeGVCFs - GCS max retries/reopens: 20

    22:57:31.198 INFO  GenotypeGVCFs - Requester pays: disabled

    22:57:31.198 INFO  GenotypeGVCFs - Initializing engine

    22:57:32.260 INFO  GenotypeGVCFs - Shutting down engine

    [26 May 2020 22:57:32 CEST] done. Elapsed time: 0.03 minutes.




    A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader



    In addition, suppose I would succeed in creating the GenotypeVCF for chr1, how do I combine this vcf with those for other chromosomes?

    Any help is more than welcome!

    Thank you in advance.



    PS: also tried the command below, based on the Gotcha's/Forum, but did not work either:

    "TILEDB_DISABLE_FILE_LOCKING=1`` gatk --java-options "-Xmx30g" GenotypeGVCFs\
    -R Reference/uT.fasta \
    -V gendb://RC_chr1 \
    -O RC_chr1_36samples.vcf


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    Update on the problem above:

    Added "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true"  to --java-options

    Apparently "A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader"

    is caused by 

    "Caused by: GenomicsDB JNI Error: GenomicsDBConfigException : Syntax error in JSON file"

    Any suggestion is moer than welcome!



    A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader



    org.broadinstitute.hellbender.exceptions.UserException: Couldn't create GenomicsDBFeatureReader

    at org.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(

    at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(

    at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(

    at org.broadinstitute.hellbender.engine.VariantLocusWalker.initializeDrivingVariants(

    at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(

    at org.broadinstitute.hellbender.engine.GATKTool.onStartup(

    at org.broadinstitute.hellbender.engine.VariantLocusWalker.onStartup(

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(

    at org.broadinstitute.hellbender.Main.runCommandLineProgram(

    at org.broadinstitute.hellbender.Main.mainEntry(

    at org.broadinstitute.hellbender.Main.main(

    Caused by: GenomicsDB JNI Error: GenomicsDBConfigException : Syntax error in JSON file /data/wannesd/RG_chr1/callset.json

    at org.genomicsdb.reader.GenomicsDBQueryStream.jniGenomicsDBInit(Native Method)

    at org.genomicsdb.reader.GenomicsDBQueryStream.<init>(

    at org.genomicsdb.reader.GenomicsDBQueryStream.<init>(

    at org.genomicsdb.reader.GenomicsDBQueryStream.<init>(

    at org.genomicsdb.reader.GenomicsDBFeatureReader.generateHeadersForQuery(

    at org.genomicsdb.reader.GenomicsDBFeatureReader.<init>(

    at org.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(

    ... 12 more

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    Tiffany Miller

    Hi @wd, sorry for the delay. 

    It appears another user was having this issue and it was due to the sample names getting altered. Does this apply to your situation?

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