picard error

[seq_GA]

While I am trying to remove duplicates for pair end data using picard,
I am getting th following errors.

I start picard as below:

java -jar /tools/SAM/picard-tools-1.13/MarkDuplicates.jar I=bin1_sorted.bam O=bin1_PCR_removed.bam M=metrics.txt ASSUME_SORTED=true REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT

Runtime.totalMemory()=1031405568
Exception in thread "main" java.lang.IllegalStateException: Invalid values for pairs and unique pairs: 1574422, 2050
at net.sf.picard.sam.DuplicationMetrics.estimateLibrarySize(DuplicationMetrics.java:90)
at net.sf.picard.sam.DuplicationMetrics.calculateDerivedMetrics(DuplicationMetrics.java:64)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:176)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:142)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:79)


Thanks.

[seq_GA]

Can anyone tell me why this is happening?

[Lv Ray]

try :
samtools view -H bin1_sorted.bam |less -S
inspect the header of your .bam file. I got the same error.