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

error for gatk -- PathSeqPipelineSpark "java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed."


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    Gökalp Çelik

    Hi haha xixi

    Did you use fastqs to align and produce bams or did you use fasta files to convert to bam? Do you observe this error with all your samples or only in a single sample?

    Before we even proceed further can you try running this with the latest GATK version 4.4? There may be fixes along the way which could have solved this problem already. 

    If none of them works as this error is a low level one in the jni library we may need a sample file to reproduce this error. Can you send us a sample file?



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