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HaplotypeCaller producing output without any vcf

I am using GATK Ubuntu 18.04 LTS and javac -version => javac 1.8.0_181.

I am basically trying to call variants from Targetted DNA sequencing data using HaplotypeCaller. Though HaplotypeCaller is executing but it is not calling any variants. Now seeing some other posts I did ensure that i have java 8 and validate bam file using picard ValidateSam, and it gave no error. I'm confused. Below is the output of the haplotypecaller run.

Using GATK jar /opt/gatk- Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /opt/gatk- HaplotypeCaller --input BV-15-186_mapto_genom_sortedRG.bam --output BV-15-186_bwa_vars.vcf --reference hg19.fa 17:31:19.630 INFO NativeLibraryLoader - Loading from jar:file:/opt/gatk-!/com/intel/gkl/native/ 17:31:29.729 INFO HaplotypeCaller - ------------------------------------------------------------ 17:31:29.730 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.8.1 17:31:29.730 INFO HaplotypeCaller - For support and documentation go to 17:31:29.731 INFO HaplotypeCaller - Executing as [email protected] on Linux v4.15.0-20-generic amd64 17:31:29.731 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v10.0.2+13-Ubuntu-1ubuntu0.18.04.2 17:31:29.732 INFO HaplotypeCaller - Start Date/Time: 15 September 2018 at 5:31:19 PM IST 17:31:29.732 INFO HaplotypeCaller - ------------------------------------------------------------ 17:31:29.732 INFO HaplotypeCaller - ------------------------------------------------------------ 17:31:29.733 INFO HaplotypeCaller - HTSJDK Version: 2.16.0 17:31:29.734 INFO HaplotypeCaller - Picard Version: 2.18.7 17:31:29.734 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:31:29.734 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:31:29.734 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:31:29.734 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:31:29.734 INFO HaplotypeCaller - Deflater: IntelDeflater 17:31:29.735 INFO HaplotypeCaller - Inflater: IntelInflater 17:31:29.735 INFO HaplotypeCaller - GCS max retries/reopens: 20 17:31:29.735 INFO HaplotypeCaller - Using google-cloud-java fork 17:31:29.735 INFO HaplotypeCaller - Initializing engine 17:31:29.884 INFO HaplotypeCaller - Done initializing engine 17:31:29.891 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 17:31:29.899 INFO NativeLibraryLoader - Loading from jar:file:/opt/gatk-!/com/intel/gkl/native/ 17:31:29.901 INFO NativeLibraryLoader - Loading from jar:file:/opt/gatk-!/com/intel/gkl/native/ 17:31:29.939 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 17:31:29.940 INFO IntelPairHmm - Available threads: 4 17:31:29.940 INFO IntelPairHmm - Requested threads: 4 17:31:29.940 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 17:31:29.965 INFO ProgressMeter - Starting traversal 17:31:29.965 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 17:31:29.971 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0 17:31:29.971 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0 17:31:29.972 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec 17:31:29.972 INFO HaplotypeCaller - Shutting down engine [15 September 2018 at 5:31:29 PM IST] done. Elapsed time: 0.17 minutes. Runtime.totalMemory()=314572800 Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method lambda$identity$d67512bf$1(Lorg/broadinstitute/hellbender/utils/read/GATKRead;)Lorg/broadinstitute/hellbender/utils/read/GATKRead; at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef at org.broadinstitute.hellbender.transformers.ReadTransformer.identity( at org.broadinstitute.hellbender.engine.GATKTool.makePreReadFilterTransformer( at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse( at org.broadinstitute.hellbender.engine.GATKTool.doWork( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain( at org.broadinstitute.hellbender.Main.runCommandLineProgram( at org.broadinstitute.hellbender.Main.mainEntry( at org.broadinstitute.hellbender.Main.main(


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