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

GenomicsDBImport throw "no tiledbgenomicsdb in java.library.path" error

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    Su Na

    By the way, hope this forum can support markdown, before-posting preview and after-posting editing. Please forgive my poor writing.

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    Bhanu Gandham

    Hi,

     

    1. Can you please tell us about your OS and hardware specs?
    2. Another thing to check is the tmp directory. Maybe its full or doesn't have access permisions?
    3. Also try to run this command " jar tvf <gatk jar file> | grep -i genomicsdb" . This is to check .so or .dylib libraries, which if missing could cause this error. 
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    Su Na

    Hi @Bhanu Gandham. Thank you for your reply and sorry for my delay. I've tried several times with different setting and/or input data, but I can not make this error to be recurrent. Anyway, it seems to me that changing default `--tmp-dir` solved this problem.

     

     

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