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SVDiscovery Errors

jacobMjacobM SydneyMember

Hi,

I am attempting to run the SVDiscovery script on 81 bams. Preprocess has worked fine, however now I am stuck with the following errors:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException
at htsjdk.samtools.SAMRecordQueryNameComparator.fileOrderCompare(SAMRecordQueryNameComparator.java:76)
at htsjdk.samtools.SAMRecordQueryNameComparator.compare(SAMRecordQueryNameComparator.java:32)
at htsjdk.samtools.SAMRecordQueryNameComparator.compare(SAMRecordQueryNameComparator.java:29)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
at java.util.TimSort.sort(TimSort.java:234)
at java.util.Arrays.sort(Arrays.java:1512)
at htsjdk.samtools.util.SortingCollection$InMemoryIterator.(SortingCollection.java:350)
at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:269)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:203)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.closeOutputFiles(DeletionDiscoveryAlgorithm.java:1155)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.close(DeletionDiscoveryAlgorithm.java:122)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:109)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:40)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5.GS-0-g797d0c5):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

and

ERROR stack trace

htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /home/569/jem569/.queue/tmp/genstrip_chr12:1-133275309:100-100000_pairsbyname1_4806193241021307727.bam
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:331)
at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:294)
at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:194)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
at htsjdk.samtools.util.BinaryCodec.writeByteBuffer(BinaryCodec.java:174)
at htsjdk.samtools.util.BinaryCodec.writeInt(BinaryCodec.java:220)
at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:121)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:127)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:204)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.closeOutputFiles(DeletionDiscoveryAlgorithm.java:1155)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.close(DeletionDiscoveryAlgorithm.java:122)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:109)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:40)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
Caused by: java.io.IOException: Disk quota exceeded
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
... 23 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5.GS-0-g797d0c5):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Write error; BinaryCodec in writemode; file: /home/569/jem569/.queue/tmp/genstrip_chr12:1-133275309:100-100000_pairsbyname1_4806193241021307727.bam
ERROR

Running on a small subset (n=5) works fine. Any advice would be greatly appreciated.

Tagged:

Best Answer

Answers

  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    A problem with the bam suggested at the end of the error message perhaps? ie. genstrip_chr12:1-133275309:100-100000_pairsbyname1_4806193241021307727.bam .. so run with about half the bam files, or check their format and quality.

    Or maybe there's a problem with specifying the chromosome co-ordinates. I did one preparation run, then bash-looped 'discovery' through the major chromosomes. You have to change the directory structure slightly from recommended.

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