The input script is like this:
java -jar /nfs/home/gatk/GenomeAnalysisTK.jar
-T GenotypeGVCFs
-R /nfs/home/tool/gatk/bundle/2.8/hg19/ucsc.hg19.fasta
--variant /home/sample/sample4/AD_1.g.vcf
--variant /home/sample/sample4/AD_2.g.vcf
--variant /home/sample/sample4/AD_3.g.vcf
--variant /home/sample/sample4/AD_4.g.vcf
-o /home/sample/sample4/AD_raw_variants.vcf
It was running smoothly, but suddenly it stopped at chr19. The screen is like this:
INFO 17:47:12,334 ProgressMeter - chr19:11563684 5.32049E7 7.6 h 8.6 m 85.1% 9.0 h 80.0 m
INFO 17:47:42,335 ProgressMeter - chr19:12766650 5.3285579E7 7.6 h 8.6 m 85.2% 9.0 h 79.8 m
INFO 17:47:47,835 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.NumberFormatException: For input string: "495"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:481)
at java.lang.Integer.parseInt(Integer.java:527)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:161)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:257)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: For input string: "495"
ERROR ------------------------------------------------------------------------------------------
jiangli@darwin:~$ ^C
The .g.vcf files are created by CombineGVCFs. So, is there anything wrong in these gVCF files?
Best Wishes,
River Lee