I am trying to combine 240 gvcf files to run joint GenotypeGVCFs. considering that I start from the same gVCF !!! Is it relative to the padding regions during HaplotypeCaller? I don't understand why in some cases/intevals I don't have errors while in other cases/intervals I have errors, during the same analysis.

(c) Malformed VCF file (or malformed index) (a) A VCF file has two lines with the same genomic position The most likely cause is unexpected data in the input file: Previous cell: current cell: [ 1, 11799997 What(): VCF2TileDBException : Incorrect cell order found - cells must be in column major order. Terminate called after throwing an instance of 'VCF2TileDBException' Processed 6 total batches in 0.2 minutes.ġ4:03:59.867 INFO GenomicsDBImport - Import of all batches to GenomicsDB completed!ġ4:03:59.956 INFO GenomicsDBImport - Shutting down engine

Then, when I'm going to create the DB wiht GenomicDBImport, with the same range of intervals, only in some in some cases I have the following error, not in all intervals!ġ4:03:59.867 INFO ProgressMeter - Traversal complete. In the HaplotypeCaller step I use 404 intervals with 100bp padding. Let me know if this is a known issue, or if it has already been fixed and I should try a different build, or if you have any questions. Elapsed time: 195.26 minutes.Įxception in thread 'main' : GC overhead limit exceededĪt (Spliterators.java:240)Īt (Arrays.java:4911)Īt (Arrays.java:5053)Īt (Arrays.java:5035)Īt .isValidConformation(GeneralPloidyExactAFCalculator.java:315)Īt .computeLofK(GeneralPloidyExactAFCalculator.java:280)Īt .calculateACConformationAndUpdateQueue(GeneralPloidyExactAFCalculator.java:187)Īt .fastCombineMultiallelicPool(GeneralPloidyExactAFCalculator.java:148)Īt .combineSinglePools(GeneralPloidyExactAFCalculator.java:112)Īt .computeLog10PNonRef(GeneralPloidyExactAFCalculator.java:25)Īt .getLog10PNonRef(AFCalculator.java:33)Īt .(GenotypingEngine.java:255)Īt .(GenotypingEngine.java:210)Īt .(GenotypeGVCFs.java:265)Īt .(GenotypeGVCFs.java:221)Īt .(GenotypeGVCFs.java:200)Īt .VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110)Īt .VariantWalkerBase$$Lambda$89/1692317071.accept(Unknown Source)Īt $ForEachOp$OfRef.accept(ForEachOps.java:184)Īt $2$1.accept(ReferencePipeline.java:175)Īt (Iterator.java:116)Īt $IteratorSpliterator.forEachRemaining(Spliterators.java:1801)Īt .copyInto(AbstractPipeline.java:481)Īt .wrapAndCopyInto(AbstractPipeline.java:471)Īt $ForEachOp.evaluateSequential(ForEachOps.java:151)Īt $ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)Īt .evaluate(AbstractPipeline.java:234)Īt .forEach(ReferencePipeline.java:418)Īt .averse(VariantWalkerBase.java:108)Īt .GATKTool.doWork(GATKTool.java:893)Īt .nTool(CommandLineProgram.java:136)Īt .CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) For redundancy, pasted here is the bottom of an error log file that shows the memory issue I'm having: 14:13:53.736 INFO GenotypeGVCFs - Shutting down engine At the above issue link, I attached several log error files for what happened when I progressively increased the number of samples I supplied. But when I CombineGVCFs -> GenotypeGVCFs on the same 108 samples, it takes over three hours, spits out a severely truncated VCF, and produces many memory errors. GATK 3.8 finishes the job in 36 seconds based on a list of GVCFs.

I commented on issue #4454 to bring up I've been having these issues. I also noticed that other uses have been reporting memory errors. I noticed that this problem only occurs as I introduced more samples. I recently upgraded to GATK 4, and have been having problems with GenotypeGVCFs.

Openjdk 1.8 151 sigsegv