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!