Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"
REQUIRED for all errors and issues:
a) GATK version used:
Using GATK jar /home/dgmgroup/Builds/GATK/gatk-package-4.0.1.1-local.jar
b) Exact command used:
gatk HaplotypeCaller -R human_g1k_b37_20.fasta -I NA12878_wgs_20.bam -O annavariants1.vcf -L 20:10000000-10200000
c) Entire program log:
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=1 -jar /home/dgmgroup/Builds/GATK/gatk-package-4.0.1.1-local.jar HaplotypeCaller -R human_g1k_b37_20.fasta -I NA12878_wgs_20.bam -O annavariants1.vcf -L 20:10000000-10200000
10:51:51.435 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/dgmgroup/Builds/GATK/gatk-package-4.0.1.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:51:52.522 INFO HaplotypeCaller - ------------------------------------------------------------
10:51:52.523 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.1.1
10:51:52.523 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
10:51:52.523 INFO HaplotypeCaller - Executing as dgmgroup@rocinante on Linux v4.18.0-25-generic amd64
10:51:52.523 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.3+7-Ubuntu-1ubuntu218.10.1
10:51:52.523 INFO HaplotypeCaller - Start Date/Time: 22 March 2023 at 10:51:51 GMT
10:51:52.523 INFO HaplotypeCaller - ------------------------------------------------------------
10:51:52.523 INFO HaplotypeCaller - ------------------------------------------------------------
10:51:52.524 INFO HaplotypeCaller - HTSJDK Version: 2.14.1
10:51:52.524 INFO HaplotypeCaller - Picard Version: 2.17.2
10:51:52.524 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
10:51:52.524 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:51:52.524 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:51:52.524 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:51:52.524 INFO HaplotypeCaller - Deflater: IntelDeflater
10:51:52.524 INFO HaplotypeCaller - Inflater: IntelInflater
10:51:52.524 INFO HaplotypeCaller - GCS max retries/reopens: 20
10:51:52.524 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
10:51:52.524 INFO HaplotypeCaller - Initializing engine
10:51:52.638 INFO IntervalArgumentCollection - Processing 200001 bp from intervals
10:51:52.641 INFO HaplotypeCaller - Done initializing engine
10:51:52.644 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
10:51:52.764 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/dgmgroup/Builds/GATK/gatk-package-4.0.1.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:51:52.765 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/dgmgroup/Builds/GATK/gatk-package-4.0.1.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
10:51:52.781 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
10:51:52.782 INFO IntelPairHmm - Available threads: 32
10:51:52.782 INFO IntelPairHmm - Requested threads: 4
10:51:52.782 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
10:51:52.805 INFO ProgressMeter - Starting traversal
10:51:52.805 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
10:51:52.809 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
10:51:52.809 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
10:51:52.809 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
10:51:52.809 INFO HaplotypeCaller - Shutting down engine
[22 March 2023 at 10:51:52 GMT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=968884224
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:221)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:266)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:277)
Hello there I'm getting this error when trying to run the HaplotypeCaller - any advice on how it could be solved will be appreciated
Thanks and kind regads,
Anna
-
Hello Anna Gatseva. It appears you are running a very old version of GATK 4 (from 2018) on your machine and the stacktrace you are seeing appears to be associated with some depricated/removed codepaths in the code. We generally do not try to support older versions like this and it is It is highly likely that upgrading to a newer version should resolve this error.
You can find newer GATK4 releases here: https://github.com/broadinstitute/gatk/tags. If you are still finding there are errors running the HaplotypeCaller on a newer release we would be happy to take a look and try to fix them for you.
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