[Samtools-help] invalid distance too far back error for picard AddOrReplaceReadGroups

[Yi, M. (NIH/N. [C] <yi...@ma...>]

Hi, Dear list:

I run into issues with the picard AddOrReplaceReadGroups as below:

The command I used as below (simplified file path for clarity):

java -Xms15g -Xmx15g  -jar /opt/nasapps/stow/picard-tools-1.49/AddOrReplaceReadGroups.jar  
INPUT=s_3_export.sorted.bam 
OUTPUT=F14_w_RG.bam 
RGID=708BRAAXX_Sample_F14 RGLB=F14_Illumina RGPL=Illumina RGPU=708BRAAXX.lane_3 RGSM=F14 RGCN=NCI-CCR_SF VALIDATION_STRINGENCY=SILENT


And I got the following error message:

Exception in thread "main" java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back
        at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112)
        at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:320)
        at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:302)
        at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:106)
        at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:175)
        at java.io.DataInputStream.read(DataInputStream.java:149)
        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:159)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:486)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
        at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
        at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
        at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:91)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:169)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
        at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
Caused by: java.util.zip.DataFormatException: invalid distance too far back
        at java.util.zip.Inflater.inflateBytes(Native Method)
        at java.util.zip.Inflater.inflate(Inflater.java:255)
        at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
        ... 20 more


In fact, I have total 19 bam files, each one works fine with picard AddOrReplaceReadGroups, only this bam file had the issue.
Any idea why is that?

Thanks a lot in advance!

Myi

ABCC
National Cancer Institute at Frederick,
Frederick, MD 21702