Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

error at FunctionEdge

naarkhoonaarkhoo Posts: 38Member

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


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,700Administrator, GATK Developer admin

    Hi there,

    It's difficult to say what might be wrong based on this information, but It looks like the call to bwa is not working properly. You should test the pipeline steps individually to find out if that's the case and where the error occurs exactly.

    Note that we don't provide support for running the DataProcessingPipeline as is, because it is meant to be an example, not a "out of the box" tool. So you'll need to troubleshoot this on your own. Good luck!

    Geraldine Van der Auwera, PhD

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