Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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

MarkDuplicatesSpark Follow

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    Ury Alon


    I'm using MarkDuplicatesSpark to merge large lane BAM files.

    The command fails with the following output:

    WARN HtsjdkReadsRddStorage: Unrecognized write option: DISABLE
    Using GATK jar /opt/bin/gatk/gatk-package-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx1000G -Xms400G -jar /opt/bin/gatk/gatk-package- MarkDuplicatesSpark --spark-master local[96] --input in.1.bam --input in.2.bam --input in.bam --input in.4.bam --input in.5.bam --input in.5.bam --output out.bam --metrics-file out.txt --create-output-bam-splitting-index false --create-output-variant-index false --tmp-dir ./tmp --output-shard-tmp-dir ./tmp/shard --QUIET false --verbosity WARNING --spark-verbosity WARN --conf --conf spark.executor.heartbeatInterval=1000s
    Command exited with non-zero status 247

    I have found no documentation for this error.  Can you please assist?




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