Abra error

[yuhongning]

Hi,
I am trying this tool to do realignment in a few regions, but got following error:
java.lang.NegativeArraySizeException
at java.lang.AbstractStringBuilder.(AbstractStringBuilder.java:64)
at java.lang.StringBuffer.(StringBuffer.java:108)
at abra.CompareToReference2.getSequence(CompareToReference2.java:400)
at abra.KmerSizeEvaluator.getBases(KmerSizeEvaluator.java:44)
at abra.KmerSizeEvaluator.identifyMinKmer(KmerSizeEvaluator.java:98)
at abra.NativeAssembler.assembleContigs(NativeAssembler.java:273)
at abra.ReAligner.processRegion(ReAligner.java:592)
at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21)
at abra.AbraRunnable.run(AbraRunnable.java:20)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)

My commandline is: java -Xmx8G -jar $ABRA --in ${inbam} --out ${outbam} --ref ${hg19} --targets ${bed} --working ~/abra/ > abra.log
Screen shots of errors and target bed file are attached. I really appreciate if you could point me possible reasons.
Thanks,
Yuhong

[mozack]

Could you please email your complete log file and bed file to lmose at unc dot edu ?

[yuhongning]

I just sent you the complete log file and bed file. Please let me know if additional information is needed. Thanks a lot!