Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Genotype GVCFs: ERROR MESSAGE: For input string: "PL"

fulyaakcimenfulyaakcimen istanbulMember
edited January 2016 in Ask the GATK team

Hi,
I am getting this error although I completed all my updates with the latest version.

INFO 05:09:39,967 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.NumberFormatException: For input string: "PL"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.valueOf(Integer.java:582)
at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:717)
at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128)
at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158)
at htsjdk.variant.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:148)
at htsjdk.variant.variantcontext.GenotypesContext.getMaxPloidy(GenotypesContext.java:431)
at htsjdk.variant.variantcontext.VariantContext.getMaxPloidy(VariantContext.java:792)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:422)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:154)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:257)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

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: "PL"

Thanks
Fulya

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @fulyaakcimen
    Hi Fulya,

    Can you please post the exact command you are running? Also, can you try validating your GVCFs with ValidateVariants?

    Thanks,
    Sheila

  • fulyaakcimenfulyaakcimen istanbulMember
    edited January 2016

    @Sheila
    Hi,
    thanks for your reply, I will check validatevariants, maybe one of my vcfs is malformed... Here is my command:
    java -Xmx45G -jar '/home/ndal/Downloads/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar' -T GenotypeGVCFs -R '/home/ndal/Desktop/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37_decoy.fasta' -D '/home/ndal/Desktop/ftp.broadinstitute.org/bundle/2.8/b37/dbsnp_138.b37.vcf' -nt 5 -o '/media/ndal/New Volume/ndal_cohort2.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1085.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1094.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1098.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1103.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1105.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1106.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1107.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1108.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1110.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1111.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1112.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1120.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1123.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1124.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1125.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1126.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1129.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1130.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1135.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1136.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1138.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1139.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1145.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1243.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1246.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1247.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/ALS20.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/ALS220.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/ALS401.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/ALS402.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/ALS856.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1265.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1307.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1030.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1031.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1032.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1035.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1036.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1038.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1039.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1042.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1050.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1051.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1052.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1053.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1054.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1056.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1057.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1058.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1060.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1062.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1069.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA1071.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1074.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1075.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1076.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1077.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1083.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1084.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca955.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA961.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca967.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca968.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca973.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca974.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA991.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA992.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA996.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/SCA997.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1010.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1011.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1021.raw.snps.indels.g.vcf' --variant '/media/ndal/New Volume/GVCF_TOTAL/sca1024.raw.snps.indels.g.vcf'

    Thanks
    Fulya

  • fulyaakcimenfulyaakcimen istanbulMember

    @Sheila
    Thanks,
    I found the mistake in variants by validatevariants.
    Best
    Fulya

Sign In or Register to comment.