java.lang.IllegalArgumentException

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  • Qualimap report for a specific chromosomes
    via by Миша Роткевич,
    • java.lang.IllegalArgumentException: Reference index 322 not found in sequence dictionary. at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:366) at net.sf.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRecordFactory.java:30) at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:201) at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:523) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:497) at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:465) at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:453) at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:255) at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:315) at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:313) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111) Caused by: java.lang.NullPointerException at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:364)
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