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GATK run time error

Hi GATK Team,

I am using GATK for whole genome sequencing analysis. While GenotypeGVCFs for vcf generation. Our workstation configuration is, 64GB RAM, 48 threads.

The following command used around 300 gvcf files

"java -Xxm48g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -nt 4 -R Homo_sapiens_assembly38.dbsnp138.vcf -V SRR000921.g.vcf.gz -V SRR000922.g.vcf.gz -V ..................."

I am getting the following error while processing chr 19th.

INFO 18:06:55,723 ProgressMeter - chr19:15026201 2.666411288E9 48.9 h 66.0 s 83.0% 58.9 h 10.0 h
INFO 18:07:55,726 ProgressMeter - chr19:15234501 2.666411288E9 48.9 h 66.0 s 83.0% 59.0 h 10.0 h
INFO 18:08:55,727 ProgressMeter - chr19:16105401 2.667411288E9 48.9 h 66.0 s 83.0% 59.0 h 10.0 h

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant289
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:248)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:82)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: htsjdk.samtools.FileTruncatedException: Premature end of file: /home/ADSP/Sub_sampling_combinegvcf/SRR006419.g.vcf.gz
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:388)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:132)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:172)
at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:172)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:389)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:45)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:158)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.(TabixFeatureReader.java:146)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:121)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
... 12 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Unable to create iterator for rod named variant289
ERROR ------------------------------------------------------------------------------------------

Please help me to fix this issues

Answers

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