gatk报错:java.lang.IllegalStateException: Read position too high for BAI bin indexing.

50b aligned to Chr1A:536904672-536904820.

        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:140)

        at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:210)

        at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyClose(AsyncSAMFileWriter.java:38)

        at htsjdk.samtools.util.AbstractAsyncWriter.close(AbstractAsyncWriter.java:89)

        at org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter.close(SAMFileGATKReadWriter.java:26)

        at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.closeTool(SplitNCigarReads.java:197)

        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1043)

        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:162)

        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)

        at org.broadinstitute.hellbender.Main.main(Main.java:291)

Caused by: htsjdk.samtools.SAMException: Exception creating BAM index for record A00821:774:H5KM3DSX2:3:1628:6551:31281 1/2 150b aligned to Chr1A:536904672-536904820.

        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:119)

        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:137)

        ... 12 more

Caused by: java.lang.IllegalStateException: Read position too high for BAI bin indexing.

        at htsjdk.samtools.SAMRecord.computeIndexingBin(SAMRecord.java:1577)

        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder$1.getIndexingBin(BAMIndexer.java:234)

        at htsjdk.samtools.BinningIndexBuilder.processFeature(BinningIndexBuilder.java:83)

        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:222)

        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:117)


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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

增加参数:--create-output-bam-index false

换最新版本:/share/work/biosoft/GATK/gatk-4.2.2.0/gatk

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