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  • GATK BaseRecalibrator ejects with no error!

    Hi Guys,
    I set GATK BaseRecalibrator going. When I check on progress it seems to have ejected! I have been kicked out to my $ and no error is displayed.

    First time at 51% through. Same command used got to 32.7%. Then 60.1%.....

    What may cause this seemingly random eject?

    Command below:

    java -Xmx8g -jar /usr/local/bin/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T BaseRecalibrator -R human.fa -I OD37.marked.realigned.fixed.bam -knownSites dbsnp_137.b37.vcf -knownSites Mills_and_1000G_gold_standard.indels.b37.sites.vcf -knownSites ALL.wgs.phase1_release_v2.20101123.snps_indels_sv.sites.vcf -o OD37_recal.grp -plots OD37_recal.grp.pdf

  • #2
    Hey,

    At least yours ejects, mine runs through without an error in two minutes and processes 0 reads with an empty list in my recal.grp. I have been trying to trouble shoot that even now. Your command line looks correct. You may need to update the GATK version you are using.

    Nino

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