If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
IncompatibleClassChangeError when running gatk BaseRecalibrator
I am using GATK's version:
$ gatk -version
Using GATK jar /home/gigiux/src/gatk/gatk-package-22.214.171.124-local.jar
$ java -version
java version "10.0.2" 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)
On an Ubuntu 16 machine. I would like to use BaseRecalibrator to recalibrate the base quality of an alignment.
I removed the BAM file's duplicates with SAMBAMBA:
sambamba markdup -r --overflow-list-size 1000000 --hash-table-size 1000000 <input>.bam <output>.bam
I created the index fasta and dictionary of the reference sequence:
samtools faidx grch38.fa
java -jar ~/src/picard/picard.jar CreateSequenceDictionary R=grch38.fa O=grch38.dict
I then ran GATK with this:
gatk BaseRecalibrator -I <file>.bam -R ~/grch38.fa --known-sites ~/grch38.vcf.gz -O <file>.tab
but I got:
[...]` 14:02:01.642 INFO BaseRecalibrator - Initializing engine` 14:02:01.935 INFO FeatureManager - Using codec VCFCodec to read file file:///home/gigiux/refSeq/human/grch38/old/grch38.vcf.gz` 14:02:01.969 WARN IndexUtils - Feature file ` "/home/gigiux/refSeq/human/grch38/old/grch38.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file 14:02:02.035 INFO BaseRecalibrator - Done initializing engine` 14:02:02.068 INFO BaseRecalibrationEngine - The covariates being used here: ` 14:02:02.069 INFO BaseRecalibrationEngine - ReadGroupCovariate` 14:02:02.069 INFO BaseRecalibrationEngine - QualityScoreCovariate` 14:02:02.069 INFO BaseRecalibrationEngine - ContextCovariate` 14:02:02.069 INFO BaseRecalibrationEngine - CycleCovariate` 14:02:02.084 INFO ProgressMeter - Starting traversal` 14:02:02.084 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute` 14:02:02.087 INFO BaseRecalibrator - Shutting down engine` [27 September 2018 at 14:02:02 CEST] ` org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.` Runtime.totalMemory()=1056964608` 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`
I think the main message is:
Exception in thread "main" java.lang.IncompatibleClassChangeError
at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef.
How can I sort this out? How could that variable be changed? (I haven't touch anything within GATK...)