Hi,
I got an “NoClassDefFoundError” when I was running MarkDuplicate. I downloaded
the .jar files from GitHub, and I tried version 1.119 and 1.128. Both reported
the same error. But “AddOrReplaceReadGroups” and “SortSam” work perfectly.
The command line I used for v1.119: java -jar
/path/to/picard/MarkDuplicates.jar I=input.bam O=output.bam
METRICS_FILE=output.txt VALIDATION_STRINGENCY=LENIENT
for v1.128: java -jar /path/to/picard/picard.jar MarkDuplicates I=input.bam
O=output.bam METRICS_FILE=output.txt VALIDATION_STRINGENCY=LENIENT
JDK version: jdk1.6.0
Anyone knows what the problem could be? Any input will be highly appreciated!
Thanks,
Zhu
Error message:
Exception in thread "main" java.lang.NoClassDefFoundError:
java/lang/ref/Finalizer$2
at java.lang.ref.Finalizer.runFinalization(Finalizer.java:144)
at java.lang.Runtime.runFinalization0(Native Method)
at java.lang.Runtime.runFinalization(Runtime.java:705)
at java.lang.System.runFinalization(System.java:967)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:58)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:49)
at htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164)
at picard.sam.DiskReadEndsMap.put(DiskReadEndsMap.java:67)
at picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:449)
at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
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