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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

Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException

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    KATHIE NGO

    Hi ,

    I also tried using the latest version GATK v4.1.8.1, and I still see the same issues. Any advice and guidance is appreciated.

    Thank you for your time and help.

    Best Regards,

    Kathie

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    Genevieve Brandt

    Hi KATHIE NGO, this error is resulting from the program running out of space to write files. You can specify a temporary directory that has more space with the option --tmp-dir. 

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    KATHIE NGO

    Hi Genevieve, 

    Thank you for your time and help. Can you please tell me where does the program write files by default, is it where the command was executed? The output BAM files are empty and we have about 2.2TB of free space in our /home directory on the server where I executed the command.

    Best Regards,

    Kathie

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    Genevieve Brandt

    Hi KATHIE NGO, it depends on your system. Some systems use an automatic temporary space that has less space than necessary for some jobs. If the --tmp-dir option does not work, please let us know so we can troubleshoot from there.

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    KATHIE NGO

    Hi Genevieve, 

    Thank you for your time and help. Specifying the option --tmp-dir solved my issue. 

    Best Regards,

    Kathie

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    Genevieve Brandt

    Thanks for the update! Glad it worked. 

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