Error while running SelectVariants
Posted in Ask the GATK team | Last updated on


Comments (3)

Hi,

I am running SelectVariants on a vcf file for removing indels >50bps. I am getting following error:

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-7-g5e89f01):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Line: chr1 2277268 rs140545544 CCACA C,CCACACA 515.33 PASS . GT:GQ:DP:PL:AD 2/2:5:21:.,.,381,.,5,0:1,12 1/1:45:21:723,45,0,.,.,.:0,15
ERROR ------------------------------------------------------------------------------------------

I am reporting error for version 2.4 as it shows actual line with problem.

Error with version 2.7

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Error parsing line: org.broad.tribble.readers.LineIteratorImpl@1b6dc6c9, for input source: /home/gaurav/Filter/Arabian_INDELS_NEXOME.vcf
ERROR ------------------------------------------------------------------------------------------

Error Stack trace for version 2.4

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: Line: chr1 2277268 rs140545544 CCACA C,CCACACA 515.33 PASS . GT:GQ:DP:PL:AD 2/2:5:21:.,.,381,.,5,0:1,12 1/1:45:21:723,45,0,.,.,.:0,15 at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:68) at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:342) at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:297) at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:261) at org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:60) at org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:42) at org.broadinstitute.sting.gatk.iterators.PushbackIterator.next(PushbackIterator.java:65) at org.broadinstitute.sting.gatk.iterators.PushbackIterator.element(PushbackIterator.java:51) at org.broadinstitute.sting.gatk.refdata.SeekableRODIterator.next(SeekableRODIterator.java:223) at org.broadinstitute.sting.gatk.refdata.SeekableRODIterator.next(SeekableRODIterator.java:66) at org.broadinstitute.sting.utils.collections.RODMergingIterator$Element.next(RODMergingIterator.java:72) at org.broadinstitute.sting.utils.collections.RODMergingIterator.next(RODMergingIterator.java:111) at org.broadinstitute.sting.gatk.datasources.providers.RodLocusView.next(RodLocusView.java:122) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:173) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:154) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:271) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:145) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91) Caused by: java.lang.NumberFormatException: For input string: "." at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:481) at java.lang.Integer.valueOf(Integer.java:582) at org.broadinstitute.variant.vcf.AbstractVCFCodec.decodeInts(AbstractVCFCodec.java:703) at org.broadinstitute.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:664) at org.broadinstitute.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:114) at org.broadinstitute.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:131) at org.broadinstitute.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:309) at org.broadinstitute.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:241) at org.broadinstitute.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:220) at org.broadinstitute.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:46) at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:65) ... 25 more

No error stack trace with version 2.7

I tried to validate vcf file using ValidateVariants too, but getting same error.


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