UnifiedGenotyper error with additional message -1

Hi, I encounter a strange error when using UnifiedGenotyper,
The command that I use is:
/usr/bin/java -Xmx4g -jar /home/shengyu_ni/bin/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /mnt/genotyping/sendru/human_g1k_v37.fasta -I bqsr.bam -o haplogroup.vcf -out_mode EMIT_ALL_SITES -gt_mode GENOTYPE_GIVEN_ALLELES -alleles /mnt/genotyping/sendru/isogg.vcf -nt 4 -ploidy 1 -L /mnt/genotyping/sendru/comprey.interval_list

and the error mesage is:

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

java.lang.ArrayIndexOutOfBoundsException: -1
at org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods.subsetToAlleles(GeneralPloidyGenotypeLikelihoods.java:380)
at org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoodsCalculationModel.getLikelihoods(GeneralPloidyGenotypeLikelihoodsCalculationModel.java:294)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:331)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:232)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
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.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
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: -1
ERROR ------------------------------------------------------------------------------------------

I already notice that it can be some compatible problem with my file: isogg.vcf, because when I replace that file with another vcf file, it runs successfully, but I can not spot what makes the difference. so I list the header of the vcf file as the following,

additionally, this vcf file works fine with realignment

fileformat=VCFv4.1

fileDate=20140131

source=isogg

isogg_BUILD_ID=2014

reference=GRCh37.p10

phasing=partial

INFO=<ID=ISOGG,Number=0,Type=Flag,Description="Used as y chromosome haplogroup in ISOGG. ">

FILTER=<ID=PASS,Description="Only pass snp is kept, the other possibles are private and investigation. ">

contig=<ID=1,assembly=b37,length=249250621>

contig=<ID=10,assembly=b37,length=135534747>

contig=<ID=11,assembly=b37,length=135006516>

contig=<ID=12,assembly=b37,length=133851895>

contig=<ID=13,assembly=b37,length=115169878>

contig=<ID=14,assembly=b37,length=107349540>

contig=<ID=15,assembly=b37,length=102531392>

contig=<ID=16,assembly=b37,length=90354753>

contig=<ID=17,assembly=b37,length=81195210>

contig=<ID=18,assembly=b37,length=78077248>

contig=<ID=19,assembly=b37,length=59128983>

contig=<ID=2,assembly=b37,length=243199373>

contig=<ID=20,assembly=b37,length=63025520>

contig=<ID=21,assembly=b37,length=48129895>

contig=<ID=22,assembly=b37,length=51304566>

contig=<ID=3,assembly=b37,length=198022430>

contig=<ID=4,assembly=b37,length=191154276>

contig=<ID=5,assembly=b37,length=180915260>

contig=<ID=6,assembly=b37,length=171115067>

contig=<ID=7,assembly=b37,length=159138663>

contig=<ID=8,assembly=b37,length=146364022>

contig=<ID=9,assembly=b37,length=141213431>

contig=<ID=GL000191.1,assembly=b37,length=106433>

contig=<ID=GL000192.1,assembly=b37,length=547496>

contig=<ID=GL000193.1,assembly=b37,length=189789>

contig=<ID=GL000194.1,assembly=b37,length=191469>

contig=<ID=GL000195.1,assembly=b37,length=182896>

contig=<ID=GL000196.1,assembly=b37,length=38914>

contig=<ID=GL000197.1,assembly=b37,length=37175>

contig=<ID=GL000198.1,assembly=b37,length=90085>

contig=<ID=GL000199.1,assembly=b37,length=169874>

contig=<ID=GL000200.1,assembly=b37,length=187035>

contig=<ID=GL000201.1,assembly=b37,length=36148>

contig=<ID=GL000202.1,assembly=b37,length=40103>

contig=<ID=GL000203.1,assembly=b37,length=37498>

contig=<ID=GL000204.1,assembly=b37,length=81310>

contig=<ID=GL000205.1,assembly=b37,length=174588>

contig=<ID=GL000206.1,assembly=b37,length=41001>

contig=<ID=GL000207.1,assembly=b37,length=4262>

contig=<ID=GL000208.1,assembly=b37,length=92689>

contig=<ID=GL000209.1,assembly=b37,length=159169>

contig=<ID=GL000210.1,assembly=b37,length=27682>

contig=<ID=GL000211.1,assembly=b37,length=166566>

contig=<ID=GL000212.1,assembly=b37,length=186858>

contig=<ID=GL000213.1,assembly=b37,length=164239>

contig=<ID=GL000214.1,assembly=b37,length=137718>

contig=<ID=GL000215.1,assembly=b37,length=172545>

contig=<ID=GL000216.1,assembly=b37,length=172294>

contig=<ID=GL000217.1,assembly=b37,length=172149>

contig=<ID=GL000218.1,assembly=b37,length=161147>

contig=<ID=GL000219.1,assembly=b37,length=179198>

contig=<ID=GL000220.1,assembly=b37,length=161802>

contig=<ID=GL000221.1,assembly=b37,length=155397>

contig=<ID=GL000222.1,assembly=b37,length=186861>

contig=<ID=GL000223.1,assembly=b37,length=180455>

contig=<ID=GL000224.1,assembly=b37,length=179693>

contig=<ID=GL000225.1,assembly=b37,length=211173>

contig=<ID=GL000226.1,assembly=b37,length=15008>

contig=<ID=GL000227.1,assembly=b37,length=128374>

contig=<ID=GL000228.1,assembly=b37,length=129120>

contig=<ID=GL000229.1,assembly=b37,length=19913>

contig=<ID=GL000230.1,assembly=b37,length=43691>

contig=<ID=GL000231.1,assembly=b37,length=27386>

contig=<ID=GL000232.1,assembly=b37,length=40652>

contig=<ID=GL000233.1,assembly=b37,length=45941>

contig=<ID=GL000234.1,assembly=b37,length=40531>

contig=<ID=GL000235.1,assembly=b37,length=34474>

contig=<ID=GL000236.1,assembly=b37,length=41934>

contig=<ID=GL000237.1,assembly=b37,length=45867>

contig=<ID=GL000238.1,assembly=b37,length=39939>

contig=<ID=GL000239.1,assembly=b37,length=33824>

contig=<ID=GL000240.1,assembly=b37,length=41933>

contig=<ID=GL000241.1,assembly=b37,length=42152>

contig=<ID=GL000242.1,assembly=b37,length=43523>

contig=<ID=GL000243.1,assembly=b37,length=43341>

contig=<ID=GL000244.1,assembly=b37,length=39929>

contig=<ID=GL000245.1,assembly=b37,length=36651>

contig=<ID=GL000246.1,assembly=b37,length=38154>

contig=<ID=GL000247.1,assembly=b37,length=36422>

contig=<ID=GL000248.1,assembly=b37,length=39786>

contig=<ID=GL000249.1,assembly=b37,length=38502>

contig=<ID=MT,assembly=b37,length=16569>

contig=<ID=X,assembly=b37,length=155270560>

contig=<ID=Y,assembly=b37,length=59373566>

CHROM POS ID REF ALT QUAL FILTER INFO

Y 2649696 M236 G T . PASS ISOGG
Y 2655180 M176 C G . PASS ISOGG
Y 2656127 Z12426 G A . PASS ISOGG
Y 2656959 L1233 G C . PASS ISOGG

Thank you.

Best Answer

Answers

  • Sorry for start the thread early today.
    I find there are errors when I generate the VCF file, and the ref sequence in the position is not correct in some lines.
    Once I correct it, everything works fine now.

    However I also need to point out the error message given by the program is misleading, and in the realignment walk, the program does not check whether the referece sequence is correct in the designated position.

    QED

Sign In or Register to comment.