java.lang.IllegalArgumentException

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  • error in samfile header
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  • SAM tools / Mailing Lists
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    • java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: chr1 at net.sf.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:62) at net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:40) at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:106) at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:181) at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152) at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83) at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158) at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
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