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I am using Queue v2.3-5, and GenomeAnalysisTK-2.3-6-gebbba25 for a couple of my Bam files, I have encountered the following error, and I was wondering what could be the reason ...
ERROR 16:14:17,964 FunctionEdge - Error: hg19/ucsc.hg19.fasta /c1193JYUa.49483._new.1.2.sai /c1193JYUa.49483._new.reverted.bam /c1193JYUa.49483._new.reverted.bam > /c1193JYUa.49483._new.1.realigned.sam ERROR 16:14:18,264 FunctionEdge - Contents of /medpop/mpg-psrl/Parabase/Projects/Seattle/c1193JYUa.49483._new.1.realigned.sam.out:
my command is as following
java -Xmx4g -Djava.io.tmpdir=/tmp/ -jar /Tools/Queue-2.3-5-g49ed93c/Queue.jar -S /Tools/Queue-2.3-6-gebbba25/DataProcessingPipeline.scala -bwa /broad/software/free/Linux/redhat_5_x86_64/pkgs/bwa_0.5.9/bwa -i /c1193JYUa.49483/c1193JYUa.49483._new.bam -R /hg19/ucsc.hg19.fasta -D hg19/dbsnp_137.hg19.vcf -p /c1193JYUa.49483/ -bwape -run > /c1193JYUa.49483/c1193JYUa.49483.gatkpipline.log
I have shortened the path for the sake of clarity ... thank you