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Mary Happ

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Latest activity by Mary Happ
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    Mary Happ commented,

    1. Community
    2. Non-Human
    3. GATK GenotypeGVCFs stuck on starting traversal

    Ok, I've updated to the newest version and I will let you know how things go there. As for your other two points - Yes, all my runs are contained to different workspaces (separate folders for each ...

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    Mary Happ commented,

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    2. Non-Human
    3. GATK GenotypeGVCFs stuck on starting traversal

    Hi Genevieve - so over the weekend I played with the memory I was requesting for the GenotypeGVCFs jobs. After increasing the requested memory to 150gb and requesting about 120 of it for Java with ...

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    Mary Happ commented,

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    2. Non-Human
    3. GATK GenotypeGVCFs stuck on starting traversal

    Hi Genevieve - A couple updates since Wednesday.  1) Running GenomicsDBImport with the --consolidate flag had some problems for me. After all batches were imported the program stalls and eventually...

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    Mary Happ commented,

    1. Community
    2. Non-Human
    3. GATK GenotypeGVCFs stuck on starting traversal

    Small update, I have found that not maxing out the java -Xms and -Xmx options with respect to the memory I request runs GenomicsDBImport much faster so for now I am creating a new database with the...

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    Mary Happ created a post,

    GATK GenotypeGVCFs stuck on starting traversal

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    I am attempting to perform WGS variant discovery in soybean on ~1500 genotypes using the HaplotypeCaller -> GenomicsDBImport -> GenotypeGVCFs tools and have ran into an issue with GenotypeGVCFs bec...

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