Dear GATK Team,
I'm using GATK and picard to call short variant from plasmodium genome paired read fastq file . I used the HaplotypeCaller package after doing duplicate marking using picard MarkDuplicates package.
This output an error during variant call by HaplotypeCaller.
Kindly help resolve this issue
below is the log of GATK HaplotypeCaller step:
Using GATK jar /home/ubuntu/gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar
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 -Xmx4g -jar /home/ubuntu/gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar HaplotypeCaller -R Pf_ref/pf_3D7_38_Genome.fasta -I ./bam_output/Day0_IJD_252_dedup.bam -O ./variant_output/Day0_IJD_252_raw_variants.g.vcf
22:44:31.686 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/ubuntu/gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:44:32.283 INFO HaplotypeCaller - ------------------------------------------------------------
22:44:32.283 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.5.1
22:44:32.284 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:32.285 INFO HaplotypeCaller - Executing as ubuntu@mrcclimbserver.vms.swansea.climb.ac.uk on Linux v4.4.0-127-generic amd64
22:44:32.286 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v9.0.1+11
22:44:32.286 INFO HaplotypeCaller - Start Date/Time: June 27, 2018 at 10:44:31 PM UTC
22:44:32.286 INFO HaplotypeCaller - ------------------------------------------------------------
22:44:32.287 INFO HaplotypeCaller - ------------------------------------------------------------
22:44:32.289 INFO HaplotypeCaller - HTSJDK Version: 2.15.1
22:44:32.289 INFO HaplotypeCaller - Picard Version: 2.18.2
22:44:32.290 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:32.290 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:32.290 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:32.290 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:32.291 INFO HaplotypeCaller - Deflater: IntelDeflater
22:44:32.291 INFO HaplotypeCaller - Inflater: IntelInflater
22:44:32.291 INFO HaplotypeCaller - GCS max retries/reopens: 20
22:44:32.291 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
22:44:32.291 INFO HaplotypeCaller - Initializing engine
22:44:32.813 INFO HaplotypeCaller - Done initializing engine
22:44:32.828 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:44:32.849 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/ubuntu/gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
22:44:32.856 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/ubuntu/gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
22:44:32.968 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:32.969 INFO IntelPairHmm - Available threads: 32
22:44:32.969 INFO IntelPairHmm - Requested threads: 4
22:44:32.969 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:33.047 INFO ProgressMeter - Starting traversal
22:44:33.048 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:33.065 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
22:44:33.066 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
22:44:33.070 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
22:44:33.070 INFO HaplotypeCaller - Shutting down engine
[June 27, 2018 at 10:44:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2147483648
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(ReadTransformer.java:30)
at org.broadinstitute.hellbender.engine.GATKTool.makePreReadFilterTransformer(GATKTool.java:288)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:266)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:994)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
regards
Archie
