Question: Gatk Error
0
gravatar for Leandro Batista
8.0 years ago by
Paris
Leandro Batista100 wrote:

Hello,

I've been using GATK tools for Bam processing and SNP calling in whole exome and whole genome sequencing data. It has been doing just fine on several samples.

Today, unexpectedly, when running CountCovariates, some gave an error it had never given before. I've searched on the internet, but apparently it is not a common error in GATK and I couldn't find an explanation.

INFO 18:29:04,407 TraversalEngine - 11:70058337 6.44e+07 62.8 m 58.5 s 14.6% 7.2 h 6.1 h INFO 18:29:34,450 TraversalEngine - 11:70419912 6.48e+07 63.3 m 58.6 s 14.6% 7.2 h 6.2 h

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR stack trace</h5>

java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112) at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:379) 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:176) at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:519) at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:626) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:493) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:483) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:449) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619) at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:33) at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:14) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.advance(SAMDataSource.java:1023) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:1004) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:936) at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71) at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:126) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:921) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:887) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71) at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState$ReadStateManager.collectPendingReads(LocusIteratorByState.java:627) at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:339) at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.hasNext(LocusIteratorByState.java:309) at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:70) at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:156) at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:125) at org.broadinstitute.sting.gatk.datasources.providers.LocusView.advance(LocusView.java:151) at org.broadinstitute.sting.gatk.datasources.providers.LocusView.hasNextLocus(LocusView.java:117) at org.broadinstitute.sting.gatk.datasources.providers.CoveredLocusView.hasNext(CoveredLocusView.java:32) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:50) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90) Caused by: java.util.zip.DataFormatException: invalid stored block lengths at java.util.zip.Inflater.inflateBytes(Native Method) at java.util.zip.Inflater.inflate(Inflater.java:238) at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96) ... 55 more

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR A GATK RUNTIME ERROR has occurred (version 1.4-37-g0b29d54):</h5> <h5>ERROR</h5> <h5>ERROR Please visit the wiki to see if this is a known problem</h5> <h5>ERROR If not, please post the error, with stack trace, to the GATK forum</h5> <h5>ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki</h5> <h5>ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa</h5> <h5>ERROR</h5> <h5>ERROR MESSAGE: java.util.zip.DataFormatException: invalid stored block lengths</h5> <h5>ERROR ------------------------------------------------------------------------------------------</h5>

If someone could give me a clue of what might be causing this, I'd be grateful.

Leandro

gatk • 3.4k views
ADD COMMENTlink written 8.0 years ago by Leandro Batista100
2
gravatar for Pierre Lindenbaum
8.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

It's seems that your bam file is corrupted or is not compressed using the BGZF format. I would run

samtools view your.bam > /dev/null

and/or

gunzip -t your.bam

to see if there's something wrong.

ADD COMMENTlink written 8.0 years ago by Pierre Lindenbaum127k
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