droazen
commented
1 day ago @polymerase2010 I see that you're running GATK 4.1.6.0, which is almost 5 years old. Can you try the latest release (4.6.0.0), and see if the error goes away? There have been many fixes and improvements to HaplotypeCaller in the past 5 years.
polymerase2010
When I use gatk haplotypecaller to get vcf from WES bam file, it stopped at somewhere of chr4. The error information is "java.lang.IllegalStateException: Never found start 0 or stop -1 given cigar 23M90D98M". Counld you help me to debug it?
My gatk version is 4.1.6.0.
All error information is as bellows:
14:47:36.134 INFO ProgressMeter - chr3:195451651 47.5 141130 2974.2 14:47:46.204 INFO ProgressMeter - chr3:195937445 47.6 141450 2970.4 14:47:56.209 INFO ProgressMeter - chr3:197401760 47.8 142070 2973.0 14:48:06.317 INFO ProgressMeter - chr4:944918 48.0 142740 2976.5 14:48:12.491 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 1.403408197 14:48:12.491 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 110.672423397 14:48:12.491 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 120.18 sec 14:48:12.492 INFO HaplotypeCaller - Shutting down engine [September 13, 2024 at 2:48:12 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 48.27 minutes. Runtime.totalMemory()=708837376 java.lang.IllegalStateException: Never found start 0 or stop -1 given cigar 23M90D98M at org.broadinstitute.hellbender.utils.read.AlignmentUtils.getBasesCoveringRefInterval(AlignmentUtils.java:204) at org.broadinstitute.hellbender.utils.haplotype.Haplotype.trim(Haplotype.java:95) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet.trimDownHaplotypes(AssemblyResultSet.java:135) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet.calculateOriginalByTrimmedHaplotypes(AssemblyResultSet.java:111) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet.trimTo(AssemblyResultSet.java:73) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:558) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:212) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206) at org.broadinstitute.hellbender.Main.main(Main.java:292) Using GATK jar /mnt/h/linuxdir/software/gatk/build/libs/gatk-package-4.1.6.0-SNAPSHOT-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 -jar /mnt/h/linuxdir/software/gatk/build/libs/gatk-package-4.1.6.0-SNAPSHOT-local.jar HaplotypeCaller -R /mnt/h/linuxdir/database/genome/human/refseq/hg19.fa -I /mnt/g/XY10023566/bwa/XY10023566.sorted.markdup.BQSR.bam -O /mnt/g/XY10023566/gatk/XY10023566.HaplotypeCaller.vcf.gz -L /mnt/h/linuxdir/database/genome/human/S07604624_hs_hg19/S07604624_Covered.bed -L /mnt/h/linuxdir/database/genome/human/grch37_exon_chrM.bed --alleles /mnt/h/linuxdir/wespipeline2.0/interestedsite/interested.sort.merged.vcf.gz