Hello,
I updated to GATK 3.7 and am seeing the following error when running a pretty simple GenotypeGVCFs command. If you'd like bug reports elsewhere (github?) i'm happy to put these there instead.
The command is basically like:
java -Xmx48g -Xms48g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R myGenome.fasta
--variant myVCF1.g.vcf.gz
--variant [total of 35 gVCFs]
-nda -nt 24 -stand_call_conf 30 --max_alternate_alleles 12 -A FractionInformativeReads
and the stack is:
13 Dec 2016 15:19:59,086 DEBUG: ##### ERROR --
13 Dec 2016 15:19:59,351 DEBUG: ##### ERROR stack trace
13 Dec 2016 15:19:59,371 DEBUG: java.util.ConcurrentModificationException
13 Dec 2016 15:19:59,392 DEBUG: at java.util.LinkedList$ListItr.checkForComodification(LinkedList.java:966)
13 Dec 2016 15:19:59,931 DEBUG: at java.util.LinkedList$ListItr.next(LinkedList.java:888)
13 Dec 2016 15:19:59,952 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:426)
13 Dec 2016 15:19:59,974 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
13 Dec 2016 15:20:00,052 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
13 Dec 2016 15:20:00,218 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
13 Dec 2016 15:20:00,251 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
13 Dec 2016 15:20:00,568 DEBUG: at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
13 Dec 2016 15:20:00,638 DEBUG: at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:326)
13 Dec 2016 15:20:00,692 DEBUG: at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:304)
13 Dec 2016 15:20:00,735 DEBUG: at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:135)
13 Dec 2016 15:20:00,750 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
13 Dec 2016 15:20:00,760 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
13 Dec 2016 15:20:01,556 DEBUG: at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
13 Dec 2016 15:20:01,569 DEBUG: at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
13 Dec 2016 15:20:01,597 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
13 Dec 2016 15:20:01,631 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
13 Dec 2016 15:20:01,644 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
13 Dec 2016 15:20:01,656 DEBUG: at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
13 Dec 2016 15:20:01,706 DEBUG: at java.util.concurrent.FutureTask.run(FutureTask.java:266)
13 Dec 2016 15:20:01,725 DEBUG: at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
13 Dec 2016 15:20:02,540 DEBUG: at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
13 Dec 2016 15:20:02,557 DEBUG: at java.lang.Thread.run(Thread.java:745)
13 Dec 2016 15:20:02,584 DEBUG: ##### ERROR ------------------------------------------------------------------------------------------
13 Dec 2016 15:20:02,956 DEBUG: ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-g56f2c1a):
13 Dec 2016 15:20:02,968 DEBUG: ##### ERROR
13 Dec 2016 15:20:02,992 DEBUG: ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
13 Dec 2016 15:20:03,031 DEBUG: ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
13 Dec 2016 15:20:03,047 DEBUG: ##### ERROR Visit our website and forum for extensive documentation and answers to
13 Dec 2016 15:20:03,058 DEBUG: ##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
13 Dec 2016 15:20:03,390 DEBUG: ##### ERROR
13 Dec 2016 15:20:03,402 DEBUG: ##### ERROR MESSAGE: Code exception (see stack trace for error itself)
13 Dec 2016 15:20:03,425 DEBUG: ##### ERROR ------------------------------------------------------------------------------------------