Hi I am getting the following error. I ran the exact same samples/pipeline a couple of weeks ago using 3.6 and it worked fine, now with 3.7 I am getting an error:
INFO 09:49:49,742 HelpFormatter - ----------------------------------------------------------------------------------
INFO 09:49:49,745 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 09:49:49,745 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 09:49:49,745 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 09:49:49,747 HelpFormatter - [Thu Feb 09 09:49:49 MST 2017] Executing on Linux 3.10.0-327.28.3.el7.x86_64 amd64
INFO 09:49:49,747 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_111-b15
INFO 09:49:49,749 HelpFormatter - Program Args: -T GenotypeGVCFs -nt 16 -R /gs0/home/martensc/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o cohen_test.vcf --variant gatk/9273.raw.snps.indels.g.vcf --variant gatk/9274.raw.snps.indels.g.vcf --variant gatk/9275.raw.snps.indels.g.vcf --variant gatk/9276.raw.snps.indels.g.vcf --variant gatk/9277.raw.snps.indels.g.vcf --variant gatk/9278.raw.snps.indels.g.vcf --variant gatk/9279.raw.snps.indels.g.vcf --variant gatk/9280.raw.snps.indels.g.vcf --variant gatk/9281.raw.snps.indels.g.vcf
INFO 09:49:49,751 HelpFormatter - Executing as martensc@ai-rmlcpu09.niaid.nih.gov on Linux 3.10.0-327.28.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-b15.
INFO 09:49:49,751 HelpFormatter - Date/Time: 2017/02/09 09:49:49
INFO 09:49:49,751 HelpFormatter - ----------------------------------------------------------------------------------
INFO 09:49:49,751 HelpFormatter - ----------------------------------------------------------------------------------
INFO 09:49:50,063 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:49:50,238 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:49:50,603 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
INFO 09:49:50,673 GenomeAnalysisEngine - Preparing for traversal
INFO 09:49:50,676 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:49:50,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:49:50,676 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:49:50,676 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
WARN 09:49:50,756 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
WARN 09:49:50,757 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 09:49:50,757 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
INFO 09:49:50,757 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
WARN 09:49:51,164 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs
WARN 09:49:53,406 ExactAFCalculator - This tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr1: 7828173 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.
ERROR --
ERROR stack trace
java.lang.NullPointerException
at java.util.LinkedList$ListItr.next(LinkedList.java:893)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:426)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:326)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:304)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:135)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
Thanks, Craig