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Re: [Samtools-help] invalid distance too far back error for picard AddOrReplaceReadGroups
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From: Yi, M. (NIH/N. [C] <yi...@ma...> - 2011-08-18 19:09:24
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Hi, Sean and Alec: Thanks for both of you for suggestions. In fact, I just did run picard ValidateSamFile on this bam file along with other "normal and good" bam files that can run through picard AddOrReplaceReadGroups. Turns out, this bam has odd behavior with ValidateSamFile. I used the following command (take out path for simplicty) java -Xms16g -Xmx16g -jar picard-tools-1.44/ValidateSamFile.jar INPUT=s_3_export.sorted.bam OUTPUT=s_3_export.sorted.bam_validReport.out IGNORE=MISSING_TAG_NM It got error message similar as for AddOrReplaceReadGroups 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) .... But it still gives output to s_3_export.sorted.bam_validReport.out file that only has one line: ERROR: Read groups is empty Whereas if I run the same command of ValidateSamFile as above for another "Good" bam file that has no problem for picard AddOrReplaceReadGroups, I did got normal output in its report file for ValidateSamFile as below: ERROR: Read groups is empty ERROR: Record 49818802, Read name NCI-GA3_39:2:120:4177:7990, CIGAR M operator maps off end of reference ERROR: Record 49818803, Read name NCI-GA3_39:2:83:12825:12531, CIGAR M operator maps off end of reference ERROR: Record 49818804, Read name NCI-GA3_39:2:9:1503:4509, CIGAR M operator maps off end of reference ERROR: Record 49818805, Read name NCI-GA3_39:2:96:18191:13964, CIGAR M operator maps off end of reference ERROR: Record 49818806, Read name NCI-GA3_39:2:7:19792:8943, CIGAR M operator maps off end of reference ERROR: Record 49818807, Read name NCI-GA3_39:2:17:10477:10243, CIGAR M operator maps off end of reference ..... Does this mean this bam file (s_3_export.sorted.bam) is bad or corrupted? It got very similar error for both picard ValidateSamFile and AddOrReplaceReadGroups command as: java.util.zip.DataFormatException: invalid distance too far back ...... Thanks again, Ming -----Original Message----- From: Alec Wysoker [mailto:al...@br...] Sent: Thursday, August 18, 2011 12:10 PM To: Davis, Sean (NIH/NCI) [E] Cc: Yi, Ming (NIH/NCI) [C]; sam...@li... Subject: Re: [Samtools-help] invalid distance too far back error for picard AddOrReplaceReadGroups Also try ValidateSamFile. -Alec On 8/18/11 12:06 PM, Sean Davis wrote: > 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 >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. 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