售后

  htsjdk.samtools.SAMException: Unexpected number of metadata chunks 3
  at htsjdk.samtools.BAMIndexMetaData.<init>(BAMIndexMetaData.java:70)
  at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:316)
  at htsjdk.samtools.DiskBasedBAMFileIndex.getSpanOverlapping(DiskBasedBAMFileIndex.java:61)
  at htsjdk.samtools.BAMFileReader.getFileSpan(BAMFileReader.java:935)
  at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:952)
  at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612)
  at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
  at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538)
  at picard.sam.ReorderSam.doWork(ReorderSam.java:158)
  at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
  at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain
  (PicardCommandLineProgramExecutor.java:25)
  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)

  原因：参考基因组过大（hisat建立索引时的后缀为.ht2l）
  办法：将project.txt中的参考基因组选项选为large，重新刷流程；
  将bam文件重新建立.csi结尾的索引；
  清空snp目录，重新投递snp脚本。