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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

[TileDB::FileSystem] Error: (write_to_file) Cannot write to file <file> errno=121(Remote I/O error)

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    Genevieve Brandt (she/her)

    Hello Naga Rajan, we have recently added an argument to GATK that improves the usability of GenomicsDBImport on shared filesystems: --genomicsdb-shared-posixfs-optimizations. Please try that option with GATK 4.1.8.1.

    Also, is your temporary directory large enough? Please try specifying a temp directory with the argument --tmp-dir, which may help as well. 

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    Naga Rajan

    Dear Genevieve,
    Many thanks for your suggestion.

    --genomicsdb-shared-posixfs-optimizations true  --batch-size <minimal no. of samples> 

    helped me to overcome the file system limitations. 

    Thanks again for your support. 

    Regards,

    Naga

     

     

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    Genevieve Brandt (she/her)

    Naga Rajan thank you for posting your solution! Glad you were able to resolve this.

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