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

[Sean D. <sd...@ma...>]

Hi, Ming.


Are you able to generate an index using samtools index on this file?
The .bam file may be corrupt and making an index is a quick way to
check.  I'm definitely not saying that I know the cause of the
problem, though.

Sean


On Thu, Aug 18, 2011 at 11:55 AM, Yi, Ming (NIH/NCI) [C]
<yi...@ma...> wrote:
> 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
>
>
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