“java.lang.NegativeArraySizeException” when I run picard_AddorReplaceReadgroups

[MissDona]

Hi all, when I run commands as follows: run_picard.sh AddOrReplaceReadGroups INPUT=64_bwaresult_headadded.bam SORT_ORDER=coordinate RGLB=default_library RGPL=illumina RGPU=default_unit RGSM=default_name VALIDATION_STRINGENCY=SILENT OUTPUT=64bwaresult.rg.bam

I got these error messages:

Sun Sep 02 23:36:48 CST 2012] net.sf.picard.sam.AddOrReplaceReadGroups INPUT=64_bwaresult_headadded.bam OUTPUT=64bwaresult.sorted.rg.bam SORT_ORDER=coordinate RGLB=default_library RGPL=illumina RGPU=default_unit RGSM=default_name VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=16000000 RGID=1 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false [Sun Sep 02 23:36:48 CST 2012] Executing as douym@x3850b on Linux 2.6.32-220.7.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_31-b04; Picard version: 1.70(1215) INFO 2012-09-02 23:36:49 AddOrReplaceReadGroups Created read group ID=1 PL=illumina LB=default_library SM=default_name

[Sun Sep 02 23:36:51 CST 2012] net.sf.picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=2058027008 FAQ: http://sourceforge.net/apps/mediawik...itle=Main_Page Exception in thread "main" java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -667232877 at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:376) at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361) at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109) at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234) at java.io.DataInputStream.read(DataInputStream.java:132) at net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394) at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371) at net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480) at net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491) at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:178) at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:523) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:497) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:487) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:446) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619) at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:91) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61) Caused by: java.lang.NegativeArraySizeException at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374) ... 19 more 64rg.e2344 lines 2-31/31 (END)

I'm confused about these messages because I run almost the same commands before and it worked. What's the problem? Thanks a lot!

[MissDona]

bam file wrong

I've solved this problem~
It seems I shouldn't filter the tag "XT:A:U" before I run picard, in which case the paired-end reads may be disconnected and result in mistake.