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

SplitNCigar reads tool is not running


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    James Emery

    Hello Niharika.  

    It sounds like there is an issue in your code attempting to make the output writer 

    Caused by: java.nio.file.NoSuchFileException: SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bam
    at java.base/sun.nio.fs.UnixException.translateToIOException(
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(
    Can you check that that directory exists on your system and is writeable? Furthermore I would suggest (if it isn't censorship) removing the # signs from your paths in case those are causing problems with java io on your system. 
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