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 .bam.parts output error (directory already exists)

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    Genevieve Brandt (she/her)

    Hi Morgan Sparks,

    Could you run this command again using the java option -DGATK_STACKTRACE_ON_USER_EXCEPTION=true? You could add it to the java options you are already using.

    Best,

    Genevieve

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    Morgan Sparks

    Genevieve-Brandt-she-her that does seem to have fixed it, should I expect to have to do this with all ___Spark related commands in gatk? Thanks!

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    Genevieve Brandt (she/her)

    No, the -DGATK_STACKTRACE_ON_USER_EXCEPTION=true is just an extra command that can help with troubleshooting user errors.

    Your problem was most likely a random issue with Spark and your machine. Glad you got it working!

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