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SortAndFixTags FileTruncatedException error

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    Beri Shifaw

    Hi Aspen,

    What is the name of your workspace? 

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    Aspen Neuro

    Woops, forgot to include it. 

    It is "pd-wgs-workspace", in the project "pd-wgs-project". 

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    Beri Shifaw

    The error you've listed isn't originating for Terra/Firecloud, its a message coming from the GATK tool, you'll be less likely to find tool errors on this forum. Instead you could try looking for error message on the GATK forum. After searching this message on the forum I came across this post: https://gatkforums.broadinstitute.org/gatk/discussion/5320/erroneous-bam-file-from-indel-realigner

    In the SortAndFixTags task there are two GATK commands, SortSam and SetNmMdAndUqTags. The GATK error above is coming from SetNmMdAndUqTags, so i would assume SortSam is ending prematurely. 

    I can't say for sure what could be wrong, but I've had issues with this task before during a update to Terra a few months back. Increasing the memory helped solve the issue, the suggested memory size is listed in the featured workspace: Germline-SNPs-Indels-GATK4-hg38. I just updated the configurations under the featured tools method repo to reflect the suggestion the memory size. 

    SortAndFixTags

    java_opt_fix "-Xms600m"
    java_opt_sort "-Xms6000m"
    mem_size "7500 MB"
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    Aspen Neuro

    Thank you! That fix worked for me. 

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